text:
. This review aims at discussing recent QSAR concepts exploring
	higher dimensions (simulation of induced fit, simultaneous exploration
	of alternative binding modes, and solvation scenarios), and their
	benefit for the drug-discovery process.},
  doi = {10.1016/j.drudis.2007.08.004},
  institution = {Department of Medicinal Chemistry and Molecular Pharmacology, Purdue
	University, West Lafayette, IN 47907, USA. mlill@purdue.edu},
  keywords = {Computer Simulation; Drug Evaluation, Preclinical; Humans; Pharmaceutical
	Preparations; Quantitative Structure-Activity Relationship; Research},
  owner = {emilio},
  pii = {S1359-6446(07)00309-1},
  pmid = {18061879},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1016/j.drudis.2007.08.004}
}

@ARTICLE{Lin:Wood:94,
  author = {Lin, C.-L. and Wood, R. H.},
  journal = {J. Comput. Chem.},
  year = {1994},
  volume = {15},
  pages = {149},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lindorff-Larsen2010,
  author = {Kresten Lindorff-Larsen and Stefano Piana and Kim Palmo and Paul
	Maragakis and John L Klepeis and Ron O Dror and David E Shaw},
  title = {Improved side-chain torsion potentials for the Amber ff99SB protein
	force field.},
  journal = {Proteins},
  year = {2010},
  volume = {78},
  pages = {1950--1958},
  number = {8},
  month = {Jun},
  abstract = {Recent advances in hardware and software have enabled increasingly
	long molecular dynamics (MD) simulations of biomolecules, exposing
	certain limitations in the accuracy of the force fields used for
	such simulations and spurring efforts to refine these force fields.
	Recent modifications to the Amber and CHARMM protein force fields,
	for example, have improved the backbone torsion potentials, remedying
	deficiencies in earlier versions. Here, we further advance simulation
	accuracy by improving the amino acid side-chain torsion potentials
	of the Amber ff99SB force field. First, we used simulations of model
	alpha-helical systems to identify the four residue types whose rotamer
	distribution differed the most from expectations based on Protein
	Data Bank statistics. Second, we optimized the side-chain torsion
	potentials of these residues to match new, high-level quantum-mechanical
	calculations. Finally, we used microsecond-timescale MD simulations
	in explicit solvent to validate the resulting force field against
	a large set of experimental NMR measurements that directly probe
	side-chain conformations. The new force field, which we have termed
	Amber ff99SB-ILDN, exhibits considerably better agreement with the
	NMR data.},
  doi = {10.1002/prot.22711},
  institution = {D. E. Shaw Research, New York, New York 10036, USA.},
  keywords = {Algorithms; Amino Acids; Animals; Cattle; Chickens; Databases, Protein;
	Magnetic Resonance Spectroscopy; Molecular Dynamics Simulation; Peptides;
	Protein Structure, Secondary; Proteins; Quantum Theory; Reproducibility
	of Results; Thermodynamics; Torsion, Mechanical},
  owner = {emilio},
  pmid = {20408171},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1002/prot.22711}
}

@ARTICLE{Linert:89,
  author = {Linert, W. and Jameson, R. F.},
  title = {The Isokinetic Relationship},
  journal = {Chem. Soc. Rev.},
  year = {1989},
  volume = {18},
  pages = {477},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Linse:Andersen:86,
  author = {Linse, P. and Andersen, H. C.},
  journal = {J. Chem. Phys.},
  year = {1986},
  volume = {85},
  pages = {3027-3041},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Liu:96,
  author = {Liu, H. and Mark, A. E. and van Gunsteren, W. F.},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {9485-9494},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Liu2006,
  author = {Pu Liu and Xuhui Huang and Ruhong Zhou and B. J. Berne},
  title = {Hydrophobic aided replica exchange: an efficient algorithm for protein
	folding in explicit solvent.},
  journal = {J Phys Chem B},
  year = {2006},
  volume = {110},
  pages = {19018--19022},
  number = {38},
  month = {Sep},
  abstract = {A hydrophobic aided replica exchange method (HAREM) is introduced
	to accelerate the simulation of all-atom protein folding in explicit
	solvent. This method is based on exaggerating the hydrophobic effect
	of various protein amino acids in water by attenuating the protein-water
	attractive interactions (mimicking the Chaperon effect) while leaving
	other interactions among protein atoms and water molecules unchanged.
	The method is applied to a small representative protein, the alpha-helix
	3K(I), and it is found that the HAREM method successfully folds the
	protein within 4 ns, while the regular replica exchange method does
	not fold the same protein within 5 ns, even with many more replicas.},
  doi = {10.1021/jp060365r},
  institution = {Department of Chemistry, Columbia University, New York, New York
	10027, USA.},
  keywords = {Algorithms; Hydrophobicity; Kinetics; Methods; Protein Folding; Solvents;
	Water},
  owner = {emilio},
  pmid = {16986898},
  timestamp = {2010.10.27},
  url = {http://dx.doi.org/10.1021/jp060365r}
}

@ARTICLE{Liu:Kim:Friesner:Berne:2005,
  author = {Liu, P. and Kim, B. and Friesner, {R. A.} and Berne, {B. J.}},
  title = {Replica exchange with solute tempering: A method for sampling biological
	systems in explicit solvent},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2005},
  volume = {102},
  pages = {13749--13754},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Liu:Baleja:2004,
  author = {Liu, Y. and Liu, Z. and Androphy, E. and Chen, J. and Baleja, {J.
	D.}},
  title = {Design and characterization of helical peptides that inhibit the
	E6 protein of papillomavirus},
  journal = {Biochemistry},
  year = {2004},
  volume = {43},
  pages = {7421-7431},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Liwo2008,
  author = {Liwo, Adam and Czaplewski, Cezary and Oldziej, Stanislaw and Scheraga,
	Harold A},
  title = {Computational techniques for efficient conformational sampling of
	proteins},
  journal = {Current Opinion in Structural Biology},
  year = {2008},
  volume = {18},
  pages = {134--139},
  number = {2},
  month = apr,
  abstract = {In this review, we summarize the computational methods for sampling
	the conformational space of biomacromolecules. We discuss the methods
	applicable to find only lowest energy conformations (global minimization
	of the potential-energy function) and to generate canonical ensembles
	(canonical Monte Carlo method and canonical molecular dynamics method
	and their extensions). Special attention is devoted to the use of
	coarse-grained models that enable simulations to be enhanced by several
	orders of magnitude.},
  booktitle = {Theory and simulation / Macromolecular assemblages},
  issn = {0959-440X},
  owner = {emilio},
  timestamp = {2011.01.13},
  url = {http://www.sciencedirect.com/science/article/B6VS6-4RN4DHM-1/2/173e1db70d82764a97c88a5cb7143af2}
}

@ARTICLE{Loftler:97,
  author = {Loftler, G. and Schreiber, H. and Steinhauser, O.},
  journal = {J. Mol. Biol.},
  year = {1997},
  volume = {270},
  pages = {520-534},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Loncharich:Brooks:89,
  author = {Loncharich, R. J. and Brooks, B.},
  journal = {Proteins: Structure, Function, and Genetics},
  year = {1989},
  volume = {6},
  pages = {32-45},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Loving2010,
  author = {Kathryn Loving and Ian Alberts and Woody Sherman},
  title = {Computational approaches for fragment-based and de novo design.},
  journal = {Curr Top Med Chem},
  year = {2010},
  volume = {10},
  pages = {14--32},
  number = {1},
  abstract = {Fragment-based and de novo design strategies have been used in drug
	discovery for years. The methodologies for these strategies are typically
	discussed separately, yet the applications of these techniques overlap
	substantially. We present a review of various fragment-based discovery
	and de novo design protocols with an emphasis on successful applications
	in real-world drug discovery projects. Furthermore, we illustrate
	the strengths and weaknesses of the various approaches and discuss
	how one method can be used to complement another. We also discuss
	how the incorporation of experimental data as constraints in computational
	models can produce novel compounds that occupy unique areas in intellectual
	property (IP) space yet are biased toward the desired chemical property
	space. Finally, we present recent research results suggesting that
	computational tools applied to fragment-based discovery and de novo
	design can have a greater impact on the discovery process when coupled
	with the right experiments.},
  institution = {Schrödinger, Inc., 120 West 45th Street, 29th Floor, New York, New
	York 10036, USA. kathryn.loving@schrodinger.com},
  keywords = {Algorithms; Computational Biology; Computer Simulation; Crystallography,
	X-Ray; Drug Design; Models, Molecular; Pharmaceutical Preparations},
  owner = {emilio},
  pii = {CTMC-Abs-002-10-1},
  pmid = {19929832},
  timestamp = {2010.10.26}
}

@ARTICLE{Lu2003,
  author = {Nandou Lu and Jhumpa Adhikari and David A Kofke},
  title = {Variational formula for the free energy based on incomplete sampling
	in a molecular simulation.},
  journal = {Phys Rev E Stat Nonlin Soft Matter Phys},
  year = {2003},
  volume = {68},
  pages = {026122},
  number = {2 Pt 2},
  month = {Aug},
  abstract = {Finite sampling in free-energy perturbation (FEP) calculations by
	molecular simulation leads to reproducible systematic errors, with
	sign shown to depend (in a known way) only on which system governs
	sampling in the simulation. Thus the result of a FEP calculation
	can be used as a bound on the true free energy. This inequality is
	of a wholly different nature from established forms such as the Gibbs-Bogoliubov
	inequality or the second law, in that its origins relate to the performance
	of a molecular simulation. If one can identify a suitable reference
	system having a free energy known as a function of some defining
	parameter, variational schemes based on the finite-sampling inequalities
	can be implemented. This idea is demonstrated through calculation
	of the free energy of a hard-sphere solid by perturbing from harmonic
	references and of a hard-sphere fluid by perturbing from infinitely
	polydisperse references. The tightness of the bounds increases with
	the amount of sampling in the simulation and correlates with the
	entropy difference between the target and reference systems. The
	bounds are tightest near the point where the entropy difference is
	least.},
  institution = {Department of Chemical Engineering, University at Buffalo, The State
	University of New York, Buffalo, New York 14260-4200, USA.},
  owner = {emilio},
  pmid = {14525064},
  timestamp = {2010.04.30}
}

@ARTICLE{Lu2001,
  author = {Lu, Nandou and Kofke, David A.},
  title = {Accuracy of free-energy perturbation calculations in molecular simulation.
	I. Modeling},
  journal = {J. Chem. Phys.},
  year = {2001},
  volume = {114},
  pages = {7303--7311},
  number = {17},
  month = may,
  keywords = {digital simulation, molecular dynamics method, entropy, chemical potential,
	perturbation theory},
  owner = {emilio},
  publisher = {AIP},
  timestamp = {2010.07.09},
  url = {http://link.aip.org/link/?JCP/114/7303/1}
}

@ARTICLE{Lu2004a,
  author = {Nandou Lu and David A Kofke and Thomas B Woolf},
  title = {Improving the efficiency and reliability of free energy perturbation
	calculations using overlap sampling methods.},
  journal = {J Comput Chem},
  year = {2004},
  volume = {25},
  pages = {28--39},
  number = {1},
  month = {Jan},
  abstract = {A challenge in free energy calculation for complex molecular systems
	by computer simulation is to obtain a reliable estimate within feasible
	computational time. In this study, we suggest an answer to this challenge
	by exploring a simple method, overlap sampling (OS), for producing
	reliable free-energy results in an efficient way. The formalism of
	the OS method is based on ensuring sampling of important overlapping
	phase space during perturbation calculations. This technique samples
	both forward and reverse free energy perturbation (FEP) to improve
	the free-energy calculation. It considers the asymmetry of the FEP
	calculation and features an ability to optimize both the precision
	and the accuracy of the measurement without affecting the simulation
	process itself. The OS method is tested at two optimization levels:
	no optimization (simple OS), and full optimization (equivalent to
	Bennett's method), and compared to conventional FEP techniques, including
	the widely used direct FEP averaging method, on three alchemical
	mutation systems: (a) an anion transformation in water solution,
	(b) mutation between methanol and ethane, and (c) alchemical change
	of an adenosine molecule. It is consistently shown that the reliability
	of free-energy estimates can be greatly improved using the OS techniques
	at both optimization levels, while the performance of Bennett's method
	is particularly striking. In addition, the efficiency of a calculation
	can be significantly improved because the method is able to (a) converge
	to the right answer quickly, and (b) work for large perturbations.
	The basic two-stage OS method can be extended to admit additional
	stages, if needed. We suggest that the OS method can be used as a
	general perturbation technique for computing free energy differences
	in molecular simulations.},
  doi = {10.1002/jcc.10369},
  institution = {Department of Physiology, School of Medicine, Johns Hopkins University,
	725 North Wolfe Street, 206 Biophysics Building, Baltimore, Maryland
	21205, USA. nlu@groucho.med.jhmi.edu},
  owner = {emilio},
  pmid = {14634991},
  timestamp = {2010.04.30},
  url = {http://dx.doi.org/10.1002/jcc.10369}
}

@ARTICLE{Lu2003a,
  author = {Lu, Nandou and Singh, Jayant K. and Kofke, David A.},
  title = {Appropriate methods to combine forward and reverse free-energy perturbation
	averages},
  journal = {J. Chem. Phys.},
  year = {2003},
  volume = {118},
  pages = {2977--2984},
  number = {7},
  month = feb,
  keywords = {free energy, water, chemical potential, Lennard-Jones potential, liquid
	theory},
  owner = {emilio},
  publisher = {AIP},
  timestamp = {2010.04.30},
  url = {http://link.aip.org/link/?JCP/118/2977/1}
}

@ARTICLE{Lu2004,
  author = {Nandou Lu and Di Wu and Thomas B Woolf and David A Kofke},
  title = {Using overlap and funnel sampling to obtain accurate free energies
	from nonequilibrium work measurements.},
  journal = {Phys Rev E Stat Nonlin Soft Matter Phys},
  year = {2004},
  volume = {69},
  pages = {057702},
  number = {5 Pt 2},
  month = {May},
  abstract = {Two concepts are presented for accurate nonequilibrium work free-energy
	measurements, realized both in molecular simulation and experiment.
	First, the need for an intermediate important to both the reference
	and the target systems (overlap) is indicated. Second, the use of
	a soft path from each end point to the intermediate (funnel) is demonstrated.
	Schemes implementing these concepts dramatically improve efficiency
	and accuracy of free energy calculations, as shown by calculation
	of the free energy of ion charging in water, and the free energy
	change in mutation of an adenosine molecule.},
  institution = {Department of Physiology, School of Medicine, Johns Hopkins University,
	Baltimore, Maryland 21205-2185, USA.},
  keywords = {Adenosine; Biophysics; Models, Statistical; Thermodynamics; Time Factors;
	Work},
  owner = {emilio},
  pmid = {15244984},
  timestamp = {2010.04.30}
}

@ARTICLE{Lu2007,
  author = {Lu, Yipin and Wang, Renxiao and Yang, Chao-Yie and Wang, Shaomeng},
  title = {Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal
	Structures of Protein-Ligand Complexes},
  journal = {J. Chem. Inf. Model.},
  year = {2007},
  volume = {47},
  pages = {668--675},
  number = {2},
  month = mar,
  abstract = {We have performed a comprehensive analysis of water molecules at the
	protein−ligand interfaces observed in 392 high-resolution crystal
	structures. There are a total of 1829 ligand-bound water molecules
	in these 392 complexes; 18% are surface water molecules, and 72%
	are interfacial water molecules. The number of ligand-bound water
	molecules in each complex structure ranges from 0 to 21 and has an
	average of 4.6. Of these interfacial water molecules, 76% are considered
	to be bridging water molecules, characterized by having polar interactions
	with both ligand and protein atoms. Among a number of factors that
	may influence the number of ligand-bound water molecules, the polar
	van der Waals (vdw) surface area of ligands has the highest Pearson
	linear correlation coefficient of 0.63. Our regression analysis predicted
	that one more ligand-bound water molecule is expected for every additional
	24 Å2 in the polar vdw surface area of the ligand. In contrast to
	the observation that the resolution is the primary factor influencing
	the number of water molecules in crystallographic models of proteins,
	we found that there is only a weak relationship between the number
	of ligand-bound water molecules and the resolution of the crystal
	structures. An analysis of the isotropic B factors of buried ligand-bound
	water molecules suggested that, when water molecules have fewer than
	two polar interactions with the protein−ligand complex, they are
	more mobile than protein atoms in the crystal structures; when they
	have more than three polar interactions, they are significantly less
	mobile than protein atoms.},
  comment = {doi: 10.1021/ci6003527},
  issn = {1549-9596},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/ci6003527}
}

@ARTICLE{Luedemann2000,
  author = {S. K. Ludemann and V. Lounnas and R. C. Wade},
  title = {How do substrates enter and products exit the buried active site
	of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic
	mapping of substrate pathways.},
  journal = {J Mol Biol},
  year = {2000},
  volume = {303},
  pages = {813--830},
  number = {5},
  month = {Nov},
  abstract = {Three possible channels by which substrates and products can exit
	from the buried active site of cytochrome P450cam have been identified
	by means of random expulsion molecular dynamics simulations. In the
	investigation described here, we computed estimates of the relative
	probabilities of ligand passage through the three channels using
	steered molecular dynamics and adiabatic mapping. For comparison,
	the same techniques are also applied to investigate substrate egress
	from cytochrome P450-BM3. The channel in cytochrome P450cam, for
	which there is the most supporting evidence from experiments (which
	we name pathway 2a), is computed to be the most probable ligand exit
	channel. It has the smallest computed unbinding work and force. For
	this channel, the ligand exits between the F/G loop and the B' helix.
	Two mechanistically distinct, but energetically similar routes through
	this channel were observed, showing that multiple pathways along
	one channel are possible. The probability of ligand exit via the
	next most probable channel (pathway 3), which is located between
	the I helix and the F and G helices, is estimated to be less than
	1/10 of the probability of exit along pathway 2a. Low-frequency modes
	of the protein extracted from an essential dynamics analysis of a
	1 ns duration molecular dynamics simulation of cytochrome P450cam
	with camphor bound, support the opening of pathway 2a on a longer
	timescale. On longer timescales, it is therefore expected that this
	pathway becomes more dominant than estimated from the present computations.},
  doi = {10.1006/jmbi.2000.4155},
  institution = {European Molecular Biology Laboratory, Meyerhofstr.1, Heidelberg,
	69117, Germany.},
  keywords = {Bacterial Proteins; Binding Sites; Camphor; Camphor 5-Monooxygenase;
	Computer Simulation; Cytochrome P-450 Enzyme System; Ethers; Fatty
	Acids, Monounsaturated; Kinetics; Ligands; Mixed Function Oxygenases;
	Models, Molecular; NADPH-Ferrihemoprotein Reductase; Probability;
	Protein Conformation; Pseudomonas putida; Static Electricity; Thermodynamics},
  owner = {emilio},
  pii = {S0022-2836(00)94155-X},
  pmid = {11061977},
  timestamp = {2010.09.07},
  url = {http://dx.doi.org/10.1006/jmbi.2000.4155}
}

@ARTICLE{Lum:Chandler:Weeks:99,
  author = {Lum, K. and Chandler, D. and Weeks, J. D.},
  title = {Hydrophobicity at small and large length scales},
  journal = {J. Phys. Chem. B},
  year = {1999},
  volume = {103},
  pages = {4570-4577},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lumry:Rajender:70,
  author = {Lumry, R. and Rajender, S.},
  title = {Enthalpy-Entropy Compensation Phenomena In Water Solutions of Proteins
	and Small Molecules: a Ubiquitous Property of Water},
  journal = {Biopolymers},
  year = {1970},
  volume = {9},
  pages = {1125-1227},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Luo2002,
  author = {Luo, Hengbin and Sharp, Kim},
  title = {On the calculation of absolute macromolecular binding free energies},
  journal = {Proceedings of the National Academy of Sciences of the United States
	of America},
  year = {2002},
  volume = {99},
  pages = {10399--10404},
  number = {16},
  abstract = {The standard framework for calculating the absolute binding free energy
	of a macromolecular association reaction A + B → AB with an association
	constant K

	AB is to equate chemical potentials of the species on the left- and
	right-hand sides of this reaction and evaluate the chemical potentials
	from theory. This theory involves (usually hidden) assumptions about
	what constitutes the bound species, AB, and where the contribution
	of the solvent appears. We present here an alternative derivation
	that can be traced back to Bjerrum, in which the expectation value
	of K

	AB is obtained directly through the statistical mechanical method
	of evaluating its ensemble (Boltzmann-weighted) average. The generalized
	Bjerrum approach more clearly delineates: (i) the different contributions
	to binding; (ii) the origin of the much-discussed and somewhat controversial
	association entropy term; and (iii) where the solvent contribution
	appears. This approach also allows approximations required for practical
	evaluation of the binding constant in complex macromolecular systems,
	to be introduced in a well defined way. We provide an example, with
	application to test cases that illustrate a range of binding behavior.},
  date = {August 6, 2002},
  owner = {emilio},
  timestamp = {2011.02.07},
  url = {http://www.pnas.org/content/99/16/10399.abstract}
}

@ARTICLE{Ludemann:Schreiberg:Abseher:Steinhauser:96,
  author = {L{\"{u}}demann, S. and Schreiberg, H. and Abseher, R. and Steinhauser,
	O.},
  title = {The Influence of Temperature on Pairwaise Hydrophobic Interactions
	of Methane-like Particles: A Molecular Dynamics Study of Free Energy},
  journal = {J. Chem. Phys.},
  year = {1996},
  volume = {104},
  pages = {286},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Prevost:Oliveira:Kocher:Wodak:96,
  author = {{Pr\'{e}vost} M. and Oliveira, I. T. and Kocher, J.-P. and Wodak,
	S. J.},
  title = {Free Energy of Cavity Formation in Liquid Water and Hexane},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {2738-43},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ma2010,
  author = {Da Ma and Peter Y Zavalij and Lyle Isaacs},
  title = {Acyclic cucurbit[n]uril congeners are high affinity hosts.},
  journal = {J Org Chem},
  year = {2010},
  volume = {75},
  pages = {4786--4795},
  number = {14},
  month = {Jul},
  abstract = {We present the design, synthesis via methylene bridged glycoluril
	tetramer building blocks, and charaterization of acyclic cucurbit[n]uril
	congeners that function as hosts for a wide variety of ammonium ions
	in water. The X-ray crystallographic characterization of the free
	host and its complexes with p-xylylenediamine and spermine establish
	the flexibility of the methylene bridged backbone of the acyclic
	cucurbit[n]uril congeners that allow them to adapt to the structural
	features of the guest. We find that the acyclic cucurbit[n]uril congeners-with
	their four contiguous methylene bridged glycoluril units and two
	aromatic o-xylylene walls bearing CO(2)H substituents-bind to ammonium
	ions in buffered water with values of K(a) ranging from approximately
	10(5) M(-1) to greater than 10(9) M(-1). Similar to the cucurbit[n]uril
	family of hosts, we find that increasing the concentration of metal
	cations in the buffer reduces the affinity of the acyclic cucurbit[n]uril
	congener toward guests by competitive binding at the ureidyl C horizontal
	lineO portals. Although the acyclic cucurbit[n]uril congeners retain
	the ability to bind to ammonium ions with high affinity, they do
	so with lower selectivity than cucurbit[n]urils presumably do to
	the structural flexibility of the hosts. A methylene bridged glycoluril
	tetramer model compound that lacks the substituted o-xylylene walls
	is a much lower affinity host, which establishes the importance of
	these rings on the overall recognition behavior of the acyclic cucurbit[n]uril
	congeners. Overall, the results in this paper establish that acyclic
	cucurbit[n]uril receptors that contain four or more contiguous methylene
	bridged glycoluril units retain many of the excellent recognition
	properties of the cucurbit[n]uril family.},
  doi = {10.1021/jo100760g},
  institution = {Department of Chemistry and Biochemistry, University of Maryland,
	College Park, Maryland 20742, USA.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {20540586},
  timestamp = {2011.10.15},
  url = {http://dx.doi.org/10.1021/jo100760g}
}

@ARTICLE{MacKerell1998,
  author = {MacKerell, A. D. and Bashford, D. and Bellott and Dunbrack, R. L.
	and Evanseck, J. D. and Field, M. J. and Fischer, S. and Gao, J.
	and Guo, H. and Ha, S. and Joseph-McCarthy, D. and Kuchnir, L. and
	Kuczera, K. and Lau, F. T. K. and Mattos, C. and Michnick, S. and
	Ngo, T. and Nguyen, D. T. and Prodhom, B. and Reiher, W. E. and Roux,
	B. and Schlenkrich, M. and Smith, J. C. and Stote, R. and Straub,
	J. and Watanabe, M. and Wiorkiewicz-Kuczera, J. and Yin, D. and Karplus,
	M.},
  title = {All-Atom Empirical Potential for Molecular Modeling and Dynamics
	Studies of Proteins},
  journal = {The Journal of Physical Chemistry B},
  year = {1998},
  volume = {102},
  pages = {3586--3616},
  number = {18},
  month = apr,
  abstract = {New protein parameters are reported for the all-atom empirical energy
	function in the CHARMM program. The parameter evaluation was based
	on a self-consistent approach designed to achieve a balance between
	the internal (bonding) and interaction (nonbonding) terms of the
	force field and among the solventsolvent, solventsolute, and solutesolute
	interactions. Optimization of the internal parameters used experimental
	gas-phase geometries, vibrational spectra, and torsional energy surfaces
	supplemented with ab initio results. The peptide backbone bonding
	parameters were optimized with respect to data for N-methylacetamide
	and the alanine dipeptide. The interaction parameters, particularly
	the atomic charges, were determined by fitting ab initio interaction
	energies and geometries of complexes between water and model compounds
	that represented the backbone and the various side chains. In addition,
	dipole moments, experimental heats and free energies of vaporization,
	solvation and sublimation, molecular volumes, and crystal pressures
	and structures were used in the optimization. The resulting protein
	parameters were tested by applying them to noncyclic tripeptide crystals,
	cyclic peptide crystals, and the proteins crambin, bovine pancreatic
	trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals.
	A detailed analysis of the relationship between the alanine dipeptide
	potential energy surface and calculated protein phi, chi angles was
	made and used in optimizing the peptide group torsional parameters.
	The results demonstrate that use of ab initio structural and energetic
	data by themselves are not sufficient to obtain an adequate backbone
	representation for peptides and proteins in solution and in crystals.
	Extensive comparisons between molecular dynamics simulations and
	experimental data for polypeptides and proteins were performed for
	both structural and dynamic properties. Energy minimization and dynamics
	simulations for crystals demonstrate that the latter are needed to
	obtain meaningful comparisons with experimental crystal structures.
	The presented parameters, in combination with the previously published
	CHARMM all-atom parameters for nucleic acids and lipids, provide
	a consistent set for condensed-phase simulations of a wide variety
	of molecules of biological interest.},
  comment = {doi: 10.1021/jp973084f},
  issn = {1520-6106},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.02.07},
  url = {http://dx.doi.org/10.1021/jp973084f}
}

@ARTICLE{Madan:Lee:94,
  author = {Madan, B. and Lee, B.},
  title = {Role of Hydrogen Bonds in Hydrophobicity: the Free Energy of Cavity
	Formation in Water Models with and without the Hydrogen Bonds},
  journal = {Biophys. Chem.},
  year = {1994},
  volume = {51},
  pages = {279-289},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Madura:Pettitt:88,
  author = {Madura, J. D. and Pettitt, B. M.},
  journal = {Chem. Phys. Lett.},
  year = {1988},
  volume = {150},
  pages = {105-108},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Majeux1999,
  author = {N. Majeux and M. Scarsi and J. Apostolakis and C. Ehrhardt and A.
	Caflisch},
  title = {Exhaustive docking of molecular fragments with electrostatic solvation.},
  journal = {Proteins},
  year = {1999},
  volume = {37},
  pages = {88--105},
  number = {1},
  month = {Oct},
  abstract = {A new method is presented for docking molecular fragments to a rigid
	protein with evaluation of the binding energy. Polar fragments are
	docked with at least one hydrogen bond with the protein while apolar
	fragments are positioned in the hydrophobic pockets. The electrostatic
	contribution to the binding energy, which consists of screened intermolecular
	energy and protein and fragment desolvation terms, is evaluated efficiently
	by a numerical approach based on the continuum dielectric approximation.
	The latter is also used to predetermine the hydrophobic pockets of
	the protein by rolling a low dielectric sphere over the protein surface
	and calculating the electrostatic desolvation of the protein and
	van der Waals interaction energy. The method was implemented in the
	program SEED (solvation energy for exhaustive docking). The SEED
	continuum electrostatic approach has been successfully validated
	by a comparison with finite difference solutions of the Poisson equation
	for more than 2,500 complexes of small molecules with thrombin and
	the monomer of HIV-1 aspartic proteinase. The fragments docked by
	SEED in the active site of thrombin reproduce the structural features
	of the interaction patterns between known inhibitors and thrombin.
	Moreover, the combinatorial connection of these fragments yields
	a number of compounds that are very similar to potent inhibitors
	of thrombin. Proteins 1999;37:88-105.},
  institution = {Department of Biochemistry, University of Zürich, Zürich, Switzerland.},
  keywords = {Computer Simulation; Drug Design; HIV Protease; HIV Protease Inhibitors;
	Humans; Hydrogen Bonding; Ligands; Models, Molecular; Poisson Distribution;
	Protein Binding; Solvents; Static Electricity; Thrombin},
  owner = {emilio},
  pii = {3.0.CO;2-O},
  pmid = {10451553},
  timestamp = {2010.04.22}
}

@ARTICLE{Majeux2001,
  author = {N. Majeux and M. Scarsi and A. Caflisch},
  title = {Efficient electrostatic solvation model for protein-fragment docking.},
  journal = {Proteins},
  year = {2001},
  volume = {42},
  pages = {256--268},
  number = {2},
  month = {Feb},
  abstract = {A method is presented for the fast evaluation of the binding energy
	of a protein-small molecule complex with electrostatic solvation.
	It makes use of a fast preprocessing step based on the assumption
	that the main contribution to electrostatic desolvation upon ligand
	binding originates from the displacement of the first shell of water
	molecules. For a rigid protein, the precomputation of the energy
	contributions on a set of grids allows the estimation of the energy
	in solution of about 300 protein-fragment binding modes per second
	on a personal computer. The docking procedure is applied to five
	rigid binding sites whose size ranges from 17 residues to a whole
	protein of 107 amino acids. Using a library of 70 mainly rigid molecules,
	known micromolar inhibitors or close analogs are docked and prioritized
	correctly. The docking based rank-ordering of the library requires
	about 5 h and is proposed as a complementary approach to structure-activity
	relationships by nuclear magnetic resonance. Proteins 2001;42:256-268.},
  institution = {Department of Biochemistry, University of Zürich, Zürich, Switzerland.},
  keywords = {Binding Sites; Caspase 1; Ligands; Mitogen-Activated Protein Kinases;
	Models, Chemical; Models, Molecular; Nuclear Proteins; Peptide Fragments;
	Protein Binding; Proto-Oncogene Proteins; Proto-Oncogene Proteins
	c-mdm2; Reproducibility of Results; Software Validation; Static Electricity;
	Tacrolimus Binding Protein 1A; Thrombin; p38 Mitogen-Activated Protein
	Kinases},
  owner = {emilio},
  pii = {3.0.CO;2-4},
  pmid = {11119650},
  timestamp = {2010.04.22}
}

@ARTICLE{Makhatadze:Privalov:96,
  author = {Makhatadze, G. I. and Privalov, P. L.},
  title = {On the Entropy of Protein Folding},
  journal = {Protein Science},
  year = {1996},
  volume = {5},
  pages = {507-510},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Makhatadze:Privalov:93,
  author = {Makhatadze, G. I. and Privalov, P. L.},
  title = {Contribution of Hydration to Protein Folding Thermodynamics. I. The
	Enthalpy of Hydration},
  journal = {J. Mol. Biol.},
  year = {1993},
  volume = {232},
  pages = {639-659},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Malmstrom:Riffle:Bonneau:Baker:2007,
  author = {Malstr\"{o}m, L. and Riffle, M. and Strauss, {C. E. M.} and Chivian,
	D. and Davis, {T. N.} and Bonneau, R. and Baker, D.},
  title = {Superfamily Assignments for the Yeast Proteome through Integration
	of Structure Prediction with the Gene Ontology},
  journal = {PLoS Biology},
  year = {2007},
  volume = {5},
  pages = {e76},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Mancera:Buckingham:95,
  author = {Mancera, R. L. and Buckingham, A. D.},
  title = {Temperature effects on the hydrophobic hydration of ethane},
  journal = {J. Phys. Chem.},
  year = {1995},
  volume = {99},
  pages = {14632-14640},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Mancera:Buckingham:95a,
  author = {Mancera, R. L. and Buckingham, A. D.},
  title = {Further evidence for a temperature-dependent hydrophobic interaction:
	the aggregation of ethane in aqueous solutions},
  journal = {Chem. Phys. Lett.},
  year = {1995},
  volume = {234},
  pages = {296-303},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Mandell:Jacobson:2007,
  author = {Mandell, D. J. and Chorny, I. and Groban, {E. S.} and Wong, {S. E.}
	and Levine, E. and Rapp, {C. S.} and Jacobson, {M. P.}},
  title = {Strengths of Hydrogen Bonds Involving Phosphorylated Amino Acid Side
	Chains. Explicit solvent pmf of ionized sidechains with OPLS.},
  journal = {J. Am. Chem. Soc.},
  year = {2007},
  volume = {129},
  pages = {820--827},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Maple2005,
  author = {Maple, Jon R. and Cao, Yixiang and Damm, Wolfgang and Halgren, Thomas
	A. and Kaminski, George A. and Zhang, Linda Y. and Friesner, Richard
	A.},
  title = {A Polarizable Force Field and Continuum Solvation Methodology for
	Modeling of Protein−Ligand Interactions},
  journal = {J. Chem. Theory Comput.},
  year = {2005},
  volume = {1},
  pages = {694--715},
  number = {4},
  month = jul,
  abstract = {A polarizable force field, and associated continuum solvation model,
	have been developed for the explicit purpose of computing and studying
	the energetics and structural features of protein binding to the
	wide range of ligands with potential for medicinal applications.
	Parameters for the polarizable force field (PFF) are derived from
	gas-phase ab initio calculations and then utilized for applications
	in which the protein binding to ligands occurs in aqueous solvents,
	wherein the charge distributions of proteins and ligands can be dramatically
	altered. The continuum solvation model is based on a self-consistent
	reaction field description of solvation, incorporating an analytical
	gradient, that allows energy minimizations (and, potentially, molecular
	dynamics simulations) of protein/ligand systems in continuum solvent.
	This technology includes a nonpolar model describing the cost of
	cavity formation, and van der Waals interactions, between the continuum
	solvent and protein/ligand solutes. Tests of the structural accuracy
	and computational stability of the methodology, and timings for energy
	minimizations of proteins and protein/ligand systems in the condensed
	phase, are reported. In addition, the derivation of polarizability,
	electrostatic, exchange repulsion, and torsion parameters from ab
	initio data is described, along with the use of experimental solvation
	energies for determining parameters for the solvation model.},
  comment = {doi: 10.1021/ct049855i},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.04.22},
  url = {http://dx.doi.org/10.1021/ct049855i}
}

@ARTICLE{Maragakis2008,
  author = {Paul Maragakis and Kresten Lindorff-Larsen and Michael P Eastwood
	and Ron O Dror and John L Klepeis and Isaiah T Arkin and Morten Ø
	Jensen and Huafeng Xu and Nikola Trbovic and Richard A Friesner and
	Arthur G Palmer Iii and David E Shaw},
  title = {Microsecond molecular dynamics simulation shows effect of slow loop
	dynamics on backbone amide order parameters of proteins.},
  journal = {J Phys Chem B},
  year = {2008},
  volume = {112},
  pages = {6155--6158},
  number = {19},
  month = {May},
  abstract = {A molecular-level understanding of the function of a protein requires
	knowledge of both its structural and dynamic properties. NMR spectroscopy
	allows the measurement of generalized order parameters that provide
	an atomistic description of picosecond and nanosecond fluctuations
	in protein structure. Molecular dynamics (MD) simulation provides
	a complementary approach to the study of protein dynamics on similar
	time scales. Comparisons between NMR spectroscopy and MD simulations
	can be used to interpret experimental results and to improve the
	quality of simulation-related force fields and integration methods.
	However, apparent systematic discrepancies between order parameters
	extracted from simulations and experiments are common, particularly
	for elements of noncanonical secondary structure. In this paper,
	results from a 1.2 micros explicit solvent MD simulation of the protein
	ubiquitin are compared with previously determined backbone order
	parameters derived from NMR relaxation experiments [Tjandra, N.;
	Feller, S. E.; Pastor, R. W.; Bax, A. J. Am. Chem. Soc. 1995, 117,
	12562-12566]. The simulation reveals fluctuations in three loop regions
	that occur on time scales comparable to or longer than that of the
	overall rotational diffusion of ubiquitin and whose effects would
	not be apparent in experimentally derived order parameters. A coupled
	analysis of internal and overall motion yields simulated order parameters
	substantially closer to the experimentally determined values than
	is the case for a conventional analysis of internal motion alone.
	Improved agreement between simulation and experiment also is encouraging
	from the viewpoint of assessing the accuracy of long MD simulations.},
  doi = {10.1021/jp077018h},
  institution = {D. E. Shaw Research, New York, New York 10036, USA.},
  keywords = {Amides; Computer Simulation; Proteins; Time Factors},
  owner = {emilio},
  pmid = {18311962},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1021/jp077018h}
}

@ARTICLE{Marcus:60,
  author = {Marcus, R. A.},
  journal = {Discuss. Faraday Soc.},
  year = {1960},
  volume = {29},
  pages = {21-56},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Marcus:Sutin:1985,
  author = {Marcus, {R. A.} and Sutin, N.},
  title = {Electron transfers in chemistry and biology},
  journal = {Biochem. Biophys. Acta},
  year = {1985},
  volume = {811},
  pages = {265--322},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Marinari:Parisi:1992,
  author = {Marinari, E. and Parisi, G.},
  title = {Simulated Tempering: A New {M}onte {C}arlo scheme},
  journal = {Europhys. Letters},
  year = {1992},
  volume = {19},
  pages = {451--458},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Friesner:Marten:96,
  author = {Marten, B. and Kim, K. and Cortis, C. and Friesner, R. A. and Murphy,
	R. B. and Ringnalda, M. N. and Sitkoff, D. and Honig, B.},
  title = {New Model for Calculation of Solvation Free Energies: Correction
	of Self-Consistent Reaction Field Continuum Dielectric Theory for
	Short-Range Hydrogen-Bonding Effects},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {11775},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Martin2005,
  author = {Philip Martin and John F Vickrey and Gheorghe Proteasa and Yurytzy
	L Jimenez and Zdzislaw Wawrzak and Mark A Winters and Thomas C Merigan
	and Ladislau C Kovari},
  title = {"Wide-open" 1.3 A structure of a multidrug-resistant HIV-1 protease
	as a drug target.},
  journal = {Structure},
  year = {2005},
  volume = {13},
  pages = {1887--1895},
  number = {12},
  month = {Dec},
  abstract = {This report examines structural changes in a highly mutated, clinical
	multidrug-resistant HIV-1 protease, and the crystal structure has
	been solved to 1.3 A resolution in the absence of any inhibitor.
	This protease variant contains codon mutations at positions 10, 36,
	46, 54, 62, 63, 71, 82, 84, and 90 that confer resistance to protease
	inhibitors. Major differences between the wild-type and the variant
	include a structural change initiated by the M36V mutation and amplified
	by additional mutations in the flaps of the protease, resulting in
	a "wide-open" structure that represents an opening that is 8 A wider
	than the "open" structure of the wild-type protease. A second structural
	change is triggered by the L90M mutation that results in reshaping
	the 23-32 segment. A third key structural change of the protease
	is due to the mutations from longer to shorter amino acid side chains
	at positions 82 and 84.},
  doi = {10.1016/j.str.2005.11.005},
  institution = {Department of Biochemistry and Molecular Biology, Wayne State University
	School of Medicine, Detroit, Michigan 48201, USA.},
  keywords = {Amino Acid Sequence; Binding Sites; Codon; Crystallography; Drug Resistance,
	Multiple, Viral; HIV Protease; HIV Protease Inhibitors; HIV-1; Molecular
	Sequence Data; Mutation; Protein Conformation; Water},
  owner = {emilio},
  pii = {S0969-2126(05)00406-5},
  pmid = {16338417},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1016/j.str.2005.11.005}
}

@ARTICLE{Martyna:Tobias:Klein:1994,
  author = {Martyna, {G. J.} and Tobias, {D. J.} and Klein, {M. L.}},
  title = {Constant pressure molecular dynamics algorithms},
  journal = {J. Comp. Phys.},
  year = {1994},
  volume = {101},
  pages = {4177-4189},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Masunov:Lazaridis:2003,
  author = {Masunov, A. and Lazaridis, T.},
  title = {Potentials of Mean Force between Ionizable Amino Acid Side Chains
	in Water},
  journal = {J. Am. Chem. Soc.},
  year = {2003},
  volume = {125},
  pages = {1722--1730},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Matubayasi:Gallicchio:Levy:98,
  author = {Matubayasi, N. and Gallicchio, E. and Levy, R. M.},
  title = {On the local and nonlocal components of solvation thermodynamics
	and their relation to solvation shell models},
  journal = {J. Chem. Phys.},
  year = {1998},
  volume = {109},
  pages = {4864-72},
  number = {12},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Matubayasi:Levy:96,
  author = {Matubayasi, N. and Levy, R. M.},
  title = {Thermodynamics of the Hydration Shell. 2. Excess Volume and Compressibility
	of a Hydrophobic Solute},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {2681},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Matubayasi:Levy:94,
  author = {Matubayasi, N. and Reed, L. H. and Levy, R. M.},
  title = {Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic
	Solute},
  journal = {J. Phys. Chem.},
  year = {1994},
  volume = {98},
  pages = {10640},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{McCammon:Straatsma:92,
  author = {J. A. McCammon and T. P. Straatsma},
  journal = {Annu. Rev. Phys. Chem.},
  year = {1992},
  volume = {43},
  pages = {407},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{McInnes2007,
  author = {Campbell McInnes},
  title = {Virtual screening strategies in drug discovery},
  journal = {Curr. Opin. Chem. Biol.},
  year = {2007},
  volume = {11},
  pages = {494--502},
  number = {5},
  month = {Oct},
  abstract = {The identification of novel therapeutic targets and characterization
	of their 3D structures is increasing at a dramatic rate. Computational
	screening methods continue to be developed and improved as credible
	and complementary alternatives to high-throughput biochemical compound
	screening (HTS). While the majority of drug candidates currently
	being developed have been found using HTS methods, high-throughput
	docking and pharmacophore-based searching algorithms are gaining
	acceptance and becoming a major source of lead molecules in drug
	discovery. Refinements and optimization of high-throughput docking
	methods have lead to improvements in reproducing experimental data
	and in hit rates obtained, validating their use in hit identification.
	In parallel with virtual screening methods, concomitant developments
	in cheminformatics including identification, design and manipulation
	of drug-like small molecule libraries have been achieved. Herein,
	currently used in silico screening techniques and their utility on
	a comparative and target dependent basis is discussed.},
  doi = {10.1016/j.cbpa.2007.08.033},
  institution = {Pharmaceutical and Biomedical Sciences, South Carolina College of
	Pharmacy, University of South Carolina, Columbia, SC 29208, USA.
	mcinnes@sccp.sc.edu},
  keywords = {Algorithms; Computational Biology; Computer Simulation; Drug Evaluation,
	Preclinical; Ligands; Protein Binding},
  owner = {emilio},
  pii = {S1367-5931(07)00117-2},
  pmid = {17936059},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1016/j.cbpa.2007.08.033}
}

@ARTICLE{Meng:Caldwell:Kollman:96,
  author = {Meng, E. C. and Caldwell, J. W. and Kollman, P. A.},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {2367},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Meng1996,
  author = {Meng, X.-L. and Wong, W. H.},
  title = {Simulating ratios of normalizing constants via a simple identity:
	A theoretical explanation},
  journal = {Statistica Sinica},
  year = {1996},
  volume = {6},
  pages = {831-860},
  comment = {From Zhiqiang},
  owner = {emilio},
  timestamp = {2011.11.06}
}

@ARTICLE{Meng2010,
  author = {Yilin Meng and Adrian E Roitberg},
  title = {Constant pH replica exchange molecular dynamics in biomolecules using
	a discrete protonation model.},
  journal = {J. Chem. Theory Comput.},
  year = {2010},
  volume = {6},
  pages = {1401--1412},
  number = {4},
  month = {Apr},
  abstract = {A constant pH replica exchange molecular dynamics (REMD) method is
	proposed and implemented to improve coupled protonation and conformational
	state sampling. By mixing conformational sampling at constant pH
	(with discrete protonation states) with a temperature ladder, this
	method avoids conformational trapping. Our method was tested and
	applied to seven different biological systems. The constant pH REMD
	not only predicted pKa correctly for small, model compounds but also
	converged faster than constant pH molecular dynamics (MD). We further
	tested our constant pH REMD on a heptapeptide from ovomucoid third
	domain (OMTKY3). Although constant pH REMD and MD produced very close
	pKa values, the constant pH REMD showed its advantage in the efficiency
	of conformational and protonation state samplings.},
  doi = {10.1021/ct900676b},
  institution = {Department of Chemistry and Quantum Theory Project. University of
	Florida Gainesville, FL 32611-8435.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {20514364},
  timestamp = {2011.01.20},
  url = {http://dx.doi.org/10.1021/ct900676b}
}

@ARTICLE{Merz:Bami:96,
  author = {Merz, K. M. and Banci, L.},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {17414-17420},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Messina:Talaga:2007,
  author = {Messina, {T. C.} and Talaga, {D. S.}},
  title = {Protein Free Energy Landscapes Remodeled by Ligand Binding},
  journal = {Biophys. J.},
  year = {2007},
  volume = {93},
  pages = {579--585},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Mezei:Beveridge:86,
  author = {Mezei, M. and Beveridge, D. L.},
  journal = {Ann. N.Y. Acad. Sci.},
  year = {1986},
  volume = {482},
  pages = {1},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Michel2010,
  author = {Julien Michel and Jonathan W Essex},
  title = {Prediction of protein-ligand binding affinity by free energy simulations:
	assumptions, pitfalls and expectations.},
  journal = {J. Comput.-Aided Mol. Des.},
  year = {2010},
  volume = {24},
  pages = {639--658},
  number = {8},
  month = {Aug},
  abstract = {Many limitations of current computer-aided drug design arise from
	the difficulty of reliably predicting the binding affinity of a small
	molecule to a biological target. There is thus a strong interest
	in novel computational methodologies that claim predictions of greater
	accuracy than current scoring functions, and at a throughput compatible
	with the rapid pace of drug discovery in the pharmaceutical industry.
	Notably, computational methodologies firmly rooted in statistical
	thermodynamics have received particular attention in recent years.
	Yet free energy calculations can be daunting to learn for a novice
	user because of numerous technical issues and various approaches
	advocated by experts in the field. The purpose of this article is
	to provide an overview of the current capabilities of free energy
	calculations and to discuss the applicability of this technology
	to drug discovery.},
  doi = {10.1007/s10822-010-9363-3},
  institution = {Institute of Structural and Molecular Biology, The University of
	Edinburgh, Edinburgh, UK. mail@julienmichel.net},
  owner = {emilio},
  pmid = {20509041},
  timestamp = {2010.09.09},
  url = {http://dx.doi.org/10.1007/s10822-010-9363-3}
}

@ARTICLE{Michel2008,
  author = {Julien Michel and Jonathan W Essex},
  title = {Hit identification and binding mode predictions by rigorous free
	energy simulations.},
  journal = {J. Med. Chem.},
  year = {2008},
  volume = {51},
  pages = {6654--6664},
  number = {21},
  month = {Nov},
  abstract = {The identification of lead molecules using computational modeling
	often relies on approximate, high-throughput approaches, of limited
	accuracy. We show here that, with a methodology we recently developed,
	it is possible to predict the relative binding free energies of structurally
	diverse ligands of the estrogen receptor-alpha using a rigorous statistical
	thermodynamics approach. Predictions obtained from the simulations
	with an explicit solvation model are in good qualitative agreement
	with experimental data, while simulations with implicit solvent models
	or rank ordering by empirical scoring functions yield predictions
	of lower quality. In addition, it is shown that free energy techniques
	can be used to select the most likely binding mode from a set of
	possible orientations generated by a docking program. It is suggested
	that the free energy techniques outlined in this study can be used
	to rank-order, by potency, structurally diverse compounds identified
	by virtual screening, de novo design or scaffold hopping programs.},
  doi = {10.1021/jm800524s},
  institution = {School of Chemistry, University of Southampton, Highfield, Southampton
	SO17 1BJ, United Kingdom.},
  keywords = {Binding Sites; Biological Products; Computer Simulation; Estradiol;
	Ligands; Models, Biological; Molecular Structure; Solvents},
  owner = {emilio},
  pmid = {18834104},
  timestamp = {2010.06.02},
  url = {http://dx.doi.org/10.1021/jm800524s}
}

@ARTICLE{Michel2009,
  author = {Julien Michel and Julian Tirado-Rives and William L Jorgensen},
  title = {Energetics of displacing water molecules from protein binding sites:
	consequences for ligand optimization.},
  journal = {J Am Chem Soc},
  year = {2009},
  volume = {131},
  pages = {15403--15411},
  number = {42},
  month = {Oct},
  abstract = {A strategy in drug design is to consider enhancing the affinity of
	lead molecules with structural modifications that displace water
	molecules from a protein binding site. Because success of the approach
	is uncertain, clarification of the associated energetics was sought
	in cases where similar structural modifications yield qualitatively
	different outcomes. Specifically, free-energy perturbation calculations
	were carried out in the context of Monte Carlo statistical mechanics
	simulations to investigate ligand series that feature displacement
	of ordered water molecules in the binding sites of scytalone dehydratase,
	p38-alphaMAP kinase, and EGFR kinase. The change in affinity for
	a ligand modification is found to correlate with the ease of displacement
	of the ordered water molecule. However, as in the EGFR example, the
	binding affinity may diminish if the free-energy increase due to
	the removal of the bound water molecule is not more than compensated
	by the additional interactions of the water-displacing moiety. For
	accurate computation of the effects of ligand modifications, a complete
	thermodynamic analysis is shown to be needed. It requires identification
	of the location of water molecules in the protein-ligand interface
	and evaluation of the free-energy changes associated with their removal
	and with the introduction of the ligand modification. Direct modification
	of the ligand in free-energy calculations is likely to trap the ordered
	molecule and provide misleading guidance for lead optimization.},
  comment = {Water},
  doi = {10.1021/ja906058w},
  institution = {Department of Chemistry, Yale University, New Haven, Connecticut
	06520, USA.},
  keywords = {Binding Sites; Hydro-Lyases; Ligands; Mitogen-Activated Protein Kinase
	14; Models, Molecular; Protein Binding; Protein Structure, Tertiary;
	Proteins; Receptor, Epidermal Growth Factor; Thermodynamics; Water},
  owner = {emilio},
  pmid = {19778066},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1021/ja906058w}
}

@ARTICLE{Michel2009a,
  author = {Julien Michel and Julian Tirado-Rives and William L Jorgensen},
  title = {Prediction of the water content in protein binding sites.},
  journal = {J Phys Chem B},
  year = {2009},
  volume = {113},
  pages = {13337--13346},
  number = {40},
  month = {Oct},
  abstract = {An efficient molecular simulation methodology has been developed to
	determine the positioning of water molecules in the binding site
	of a protein or protein-ligand complex. Occupancies and absolute
	binding free energies of water molecules are computed using a statistical
	thermodynamics approach. The methodology, referred to as Just Add
	Water Molecules (JAWS), features "theta-water" molecules that can
	appear and disappear on a binding-site grid. Key approximations render
	the technique far more efficient than conventional free energy simulations.
	Testing of JAWS on five diverse examples (neuraminidase, scytalone
	dehydratase, major urinary protein 1, beta-lactoglobulin, and COX-2)
	demonstrates its accuracy in locating hydration sites in comparison
	to results from high-resolution crystal structures. Possible applications
	include aid in refinement of protein crystal structures, drug lead
	optimization, setup of docking calculations, and simulations of protein-ligand
	complexes.},
  comment = {Water},
  doi = {10.1021/jp9047456},
  institution = {Department of Chemistry, Yale University, New Haven, CT 06520, USA.},
  keywords = {Animals; Binding Sites; Cattle; Computer Simulation; Cyclooxygenase
	2; Hydro-Lyases; Lactoglobulins; Models, Molecular; Neuraminidase;
	Protein Binding; Proteins; Solvents; Thermodynamics; Water},
  owner = {emilio},
  pmid = {19754086},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1021/jp9047456}
}

@ARTICLE{Michel2009cosb,
  author = {Julien Michel and Julian Tirado-Rives and William L Jorgensen},
  title = {Energetics of displacing water molecules from protein binding sites:
	consequences for ligand optimization.},
  journal = {J Am Chem Soc},
  year = {2009},
  volume = {131},
  pages = {15403--15411},
  number = {42},
  month = {Oct},
  note = {* A thermodynamic cycle is employed to study the thermodynamic effect
	of displacing water molecules from the binding site. The procedure
	explicitly included the alchemical processes of transforming one
	ligand into another with or without a key water molecule present
	and, in addition, the process of transfer of the water molecule from
	the binding site to the bulk by double decoupling. While simple steric
	consideration rationalize some of the results, It is shown that often
	water displacement favors or disfavors binding depending on the subtleties
	of specific molecular interactions.},
  abstract = {A strategy in drug design is to consider enhancing the affinity of
	lead molecules with structural modifications that displace water
	molecules from a protein binding site. Because success of the approach
	is uncertain, clarification of the associated energetics was sought
	in cases where similar structural modifications yield qualitatively
	different outcomes. Specifically, free-energy perturbation calculations
	were carried out in the context of Monte Carlo statistical mechanics
	simulations to investigate ligand series that feature displacement
	of ordered water molecules in the binding sites of scytalone dehydratase,
	p38-alphaMAP kinase, and EGFR kinase. The change in affinity for
	a ligand modification is found to correlate with the ease of displacement
	of the ordered water molecule. However, as in the EGFR example, the
	binding affinity may diminish if the free-energy increase due to
	the removal of the bound water molecule is not more than compensated
	by the additional interactions of the water-displacing moiety. For
	accurate computation of the effects of ligand modifications, a complete
	thermodynamic analysis is shown to be needed. It requires identification
	of the location of water molecules in the protein-ligand interface
	and evaluation of the free-energy changes associated with their removal
	and with the introduction of the ligand modification. Direct modification
	of the ligand in free-energy calculations is likely to trap the ordered
	molecule and provide misleading guidance for lead optimization.},
  comment = {Water},
  doi = {10.1021/ja906058w},
  institution = {Department of Chemistry, Yale University, New Haven, Connecticut
	06520, USA.},
  keywords = {Binding Sites; Hydro-Lyases; Ligands; Mitogen-Activated Protein Kinase
	14; Models, Molecular; Protein Binding; Protein Structure, Tertiary;
	Proteins; Receptor, Epidermal Growth Factor; Thermodynamics; Water},
  owner = {emilio},
  pmid = {19778066},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1021/ja906058w}
}

@ARTICLE{Michel2007,
  author = {Michel, Julien and Verdonk, Marcel L. and Essex, Jonathan W.},
  title = {Protein-Ligand Complexes: Computation of the Relative Free Energy
	of Different Scaffolds and Binding Modes},
  journal = {Journal of Chemical Theory and Computation},
  year = {2007},
  volume = {3},
  pages = {1645--1655},
  number = {5},
  month = sep,
  abstract = {A methodology for the calculation of the free energy difference between
	a pair of molecules of arbitrary topology is proposed. The protocol
	relies on a dual-topology paradigm, a softening of the intermolecular
	interactions, and a constraint that prevents the perturbed molecules
	from drifting away from each other at the end states. The equivalence
	and the performance of the methodology against a single-topology
	approach are demonstrated on a pair of harmonic oscillators, the
	calculation of the relative solvation free energy of ethane and methanol,
	and the relative binding free energy of two congeneric inhibitors
	of cyclooxygenase 2. The stability of two alternative binding modes
	of an inhibitor of cyclin-dependent kinase 2 is then investigated.
	Finally, the relative binding free energy of two structurally different
	inhibitors of cyclin-dependent kinase 2 is calculated. The proposed
	methodology allows the study of a range of problems that are beyond
	the reach of traditional relative free energy calculation protocols
	and should prove useful in drug design studies.},
  comment = {doi: 10.1021/ct700081t},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/ct700081t}
}

@ARTICLE{Michel2006,
  author = {Michel, Julien and Verdonk, Marcel L. and Essex, Jonathan W.},
  title = {Protein-Ligand Binding Affinity Predictions by Implicit Solvent Simulations:
	A Tool for Lead Optimization?},
  journal = {J. Med. Chem.},
  year = {2006},
  volume = {49},
  pages = {7427--7439},
  number = {25},
  month = dec,
  abstract = {Continuum electrostatics is combined with rigorous free-energy calculations
	in an effort to deliver a reliable and efficient method for in silico
	lead optimization. The methodology is tested by calculation of the
	relative binding free energies of a set of inhibitors of neuraminidase,
	cyclooxygenase2, and cyclin-dependent kinase 2. The calculated free
	energies are compared to the results obtained with explicit solvent
	simulations and empirical scoring functions. For cyclooxygenase2,
	deficiencies in the continuum electrostatics theory are identified
	and corrected with a modified simulation protocol. For neuraminidase,
	it is shown that a continuum representation of the solvent leads
	to markedly different protein−ligand interactions compared to the
	explicit solvent simulations, and a reconciliation of the two protocols
	is problematic. Cyclin-dependent kinase 2 proves more challenging,
	and none of the methods employed in this study yield high quality
	predictions. Despite the differences observed, for these systems,
	the use of an implicit solvent framework to predict the ranking of
	congeneric inhibitors to a protein is shown to be faster, as accurate
	or more accurate than the explicit solvent protocol, and superior
	to empirical scoring schemes.},
  comment = {doi: 10.1021/jm061021s},
  issn = {0022-2623},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/jm061021s}
}

@ARTICLE{Mihailescu2004,
  author = {Mihail Mihailescu and Michael K Gilson},
  title = {On the theory of noncovalent binding.},
  journal = {Biophys. J.},
  year = {2004},
  volume = {87},
  pages = {23--36},
  number = {1},
  month = {Jul},
  abstract = {It is widely accepted that the binding constant of a receptor and
	ligand can be written as a two-body integral involving the interaction
	energy of the receptor and the ligand. Interestingly, however, three
	different theories of binding in the literature dictate three distinct
	integrals. The present study uses theory, as well as simulations
	of binding experiments, to test the validity of the three integrals.
	When binding is measured by a signal that detects the ligand in the
	binding site, the most accurate results are obtained by an integral
	of the Boltzmann factor, where the bound complex is defined in terms
	of an exclusive binding region. A novel prediction of this approach,
	that expanding a ligand can increase its binding constant, is borne
	out by the simulations. The simulations also show that abnormal binding
	isotherms can be obtained when the region over which the signal is
	detected deviates markedly from the exclusion zone. Interestingly,
	the binding constant measured by equilibrium dialysis, rather than
	by monitoring a localized signal, can yield a binding constant that
	differs from that obtained from a signal measurement, and that is
	matched best by the integral of the Mayer factor.},
  doi = {10.1529/biophysj.103.031682},
  institution = {Center for Advanced Research in Biotechnology, University of Maryland
	Biotechnology Institute, Rockville, 20850, USA.},
  keywords = {Algorithms; Computer Simulation; Ligands; Models, Theoretical; Protein
	Binding},
  owner = {emilio},
  pii = {S0006-3495(04)73493-1},
  pmid = {15240441},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1529/biophysj.103.031682}
}

@ARTICLE{Min2011,
  author = {Min, Donghong and Chen, Mengen and Zheng, Lianqing and Jin, Yonghao
	and Schwartz, Martin A. and Sang, Qing-Xiang Amy and Yang, Wei},
  title = {Enhancing QM/MM Molecular Dynamics Sampling in Explicit Environments
	via an Orthogonal-Space-Random-Walk-Based Strategy},
  journal = {J. Phys. Chem. B},
  year = {2011},
  volume = {115},
  pages = {3924--3935},
  number = {14},
  month = apr,
  abstract = {null},
  comment = {doi: 10.1021/jp109454q},
  issn = {1520-6106},
  owner = {mauro},
  publisher = {American Chemical Society},
  timestamp = {2011.09.22},
  url = {http://dx.doi.org/10.1021/jp109454q}
}

@ARTICLE{Min2007,
  author = {Donghong Min and Hongzhi Li and Guohui Li and Ryan Bitetti-Putzer
	and Wei Yang},
  title = {Synergistic approach to improve ``alchemical'' free energy calculation
	in rugged energy surface},
  journal = {The Journal of Chemical Physics},
  year = {2007},
  volume = {126},
  pages = {144109},
  number = {14},
  eid = {144109},
  doi = {10.1063/1.2715950},
  keywords = {surface energy; free energy; convergence; replica techniques},
  numpages = {12},
  owner = {emilio},
  publisher = {AIP},
  timestamp = {2011.02.03},
  url = {http://link.aip.org/link/?JCP/126/144109/1}
}

@ARTICLE{Minh2005,
  author = {David D L Minh and Jennifer M Bui and Chia-En Chang and Tushar Jain
	and Jessica M J Swanson and J. Andrew McCammon},
  title = {The entropic cost of protein-protein association: a case study on
	acetylcholinesterase binding to fasciculin-2.},
  journal = {Biophys J},
  year = {2005},
  volume = {89},
  pages = {L25--L27},
  number = {4},
  month = {Oct},
  doi = {10.1529/biophysj.105.069336},
  keywords = {Acetylcholinesterase, analysis/chemistry; Binding Sites; Computer
	Simulation; Elapid Venoms, analysis/chemistry; Energy Transfer; Entropy;
	Models, Chemical; Models, Molecular; Motion; Protein Binding},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {S0006-3495(05)72861-7},
  pmid = {16100267},
  timestamp = {2011.02.03},
  url = {http://dx.doi.org/10.1529/biophysj.105.069336}
}

@ARTICLE{Mitsutake2010,
  author = {Mitsutake, Ayori and Mori, Yoshiharu and Okamoto, Yuko},
  title = {Multi-dimensional multicanonical algorithm, simulated tempering,
	replica-exchange method, and all that},
  journal = {Physics Procedia},
  year = {2010},
  volume = {4},
  pages = {89--105},
  abstract = {We discuss multi-dimensional generalizations of multicanonical algorithm,
	simulated tempering, and replica-exchange method. We generalize the
	original potential energy function E0 by adding any physical quantity
	V of interest as a new energy term with a coupling constant [lambda].
	We then perform a multi-dimensional multicanonical simulation where
	a random walk in E0 and V space is realized. We can alternately perform
	a multi-dimensional simulated-tempering simulation where a random
	walk in temperature T and parameter [lambda] is realized. The results
	of the multi-dimensional replica-exchange simulations can be used
	to determine the weight factors for these multi-dimensional multicanonical
	and simulated tempering simulations. Two examples of the above methods
	are presented for biomoleculr systems where the parameter [lambda]
	corresponds to the solvation parameter and the pressure. In the former,
	a random walk in the conformational energy and solvation free energy
	is performed, and in the latter, a random walk in the potential energy
	and volume is realized.},
  booktitle = {Recent Developments in Computer Simulation Studies in Condensed Matter
	Physics},
  issn = {1875-3892},
  keywords = {Generalized-ensemble algorithms, Multicanonical algorithm, Simulated
	tempering, Replica-exchange method, Parallel tempering, Mont Carlo,
	Molecular dynamics},
  owner = {emilio},
  timestamp = {2011.01.13},
  url = {http://www.sciencedirect.com/science/article/B8JJ4-50V1MF0-C/2/78d5d4bf62262a9793dba60068903d4f}
}

@ARTICLE{Mitsutake:Okamoto:2004,
  author = {Mitsutake, A. and Okamoto, Y.},
  title = {Replica-Exchange extensions of simulated tempering method},
  journal = {J. Chem. Phys.},
  year = {2004},
  volume = {121},
  pages = {2491--2504},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Miyata:Hirata:2008,
  author = {Miyata, T. and Hirata, F.},
  title = {Combination of Molecular Dynamics Method and 3d-RISM Theory for Conformational
	Sampling of Large Flexible Molecules in Solution},
  journal = {J. Comp. Chem.},
  year = {2008},
  volume = {29},
  pages = {871--882},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Miyata2010,
  author = {Miyata, T. and Ikuta, Y. and Hirata, F.},
  title = {Free energy calculation using molecular dynamics simulation combined
	with the three dimensional reference interaction site model theory.
	I. Free energy perturbation and thermodynamic integration along a
	coupling parameter},
  journal = {J. Chem. Phys.},
  year = {2010},
  volume = {133},
  pages = {044114},
  number = {4},
  abstract = {This article proposes a free energy calculation method based on the
	molecular dynamics simulation combined with the three dimensional
	reference interaction site model theory. This study employs the free
	energy perturbation (FEP) and the thermodynamic integration (TDI)
	along the coupling parameters to control the interaction potential.
	To illustrate the method, we applied it to a complex formation process
	in aqueous solutions between a crown ether molecule 18-Crown-6 (18C6)
	and a potassium ion as one of the simplest model systems. Two coupling
	parameters were introduced to switch the Lennard-Jones potential
	and the Coulomb potential separately. We tested two coupling procedures:
	one is a "sequential-coupling" to couple the Lennard-Jones interaction
	followed by the Coulomb coupling, and the other is a "mixed-coupling"
	to couple both the Lennard-Jones and the Coulomb interactions together
	as much as possible. The sequential-coupling both for FEP and TDI
	turned out to be accurate and easily handled since it was numerically
	well-behaved. Furthermore, it was found that the sequential-coupling
	had relatively small statistical errors. TDI along the mixed-coupling
	integral path was to be carried out carefully, paying attention to
	a numerical behavior of the integrand. The present model system exhibited
	a nonmonotonic behavior in the integrands for TDI along the mixed-coupling
	integral path and also showed a relatively large statistical error.
	A coincidence within a statistical error was obtained among the results
	of the free energy differences evaluated by FEP, TDI with the sequential-coupling,
	and TDI with the mixed-coupling. The last one is most attractive
	in terms of the computer power and is accurate enough if one uses
	a proper set of windows, taking the numerical behavior of the integrands
	into account. TDI along the sequential-coupling integral path would
	be the most convenient among the methods we tested, since it seemed
	to be well-balanced between the computational load and the accuracy.
	The numerical results reported in this article qualitatively agree
	with the experimental data for the potassium ion recognition by the
	18C6 in aqueous solution.},
  address = {Department of Theoretical and Computational Molecular Science, Institute
	for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi
	444-8585, Japan.},
  comment = {Jul 28

	Free energy calculation using molecular dynamics simulation combined
	with the three dimensional reference interaction site model theory.
	I. Free energy perturbation and thermodynamic integration along a
	coupling parameter

	20687640

	Miyata, Tatsuhiko Ikuta, Yasuhiro Hirata, Fumio United States The
	Journal of chemical physics J Chem Phys. 2010 Jul 28;133(4):044114.

	eng},
  issn = {1089-7690 (Electronic) 0021-9606 (Linking)},
  owner = {mauro},
  refid = {41},
  timestamp = {2011.07.22},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20687640}
}

@ARTICLE{Mobley2012,
  author = {David L Mobley},
  title = {Let's get honest about sampling.},
  journal = {J Comput Aided Mol Des},
  year = {2012},
  volume = {26},
  pages = {93--95},
  number = {1},
  month = {Jan},
  abstract = {Molecular simulations see widespread and increasing use in computation
	and molecular design, especially within the area of molecular simulations
	applied to biomolecular binding and interactions, our focus here.
	However, force field accuracy remains a concern for many practitioners,
	and it is often not clear what level of accuracy is really needed
	for payoffs in a discovery setting. Here, I argue that despite limitations
	of today's force fields, current simulation tools and force fields
	now provide the potential for real benefits in a variety of applications.
	However, these same tools also provide irreproducible results which
	are often poorly interpreted. Continued progress in the field requires
	more honesty in assessment and care in evaluation of simulation results,
	especially with respect to convergence.},
  doi = {10.1007/s10822-011-9497-y},
  institution = {48, USA, dmobley@gmail.com.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {22113833},
  timestamp = {2012.02.28},
  url = {http://dx.doi.org/10.1007/s10822-011-9497-y}
}

@ARTICLE{Mobley2007,
  author = {David L Mobley and John D Chodera and Ken A Dill},
  title = {The Confine-and-Release Method: Obtaining Correct Binding Free Energies
	in the Presence of Protein Conformational Change.},
  journal = {J. Chem. Theory Comput.},
  year = {2007},
  volume = {3},
  pages = {1231--1235},
  number = {4},
  abstract = {Free energy calculations are increasingly being used to estimate absolute
	and relative binding free energies of ligands to proteins. However,
	computed free energies often appear to depend on the initial protein
	conformation, indicating incomplete sampling. This is especially
	true when proteins can change conformation on ligand binding, as
	free energies associated with these conformational changes are either
	ignored or assumed to be included by virtue of the sampling performed
	in the calculation. Here, we show that, in a model protein system
	(a designed binding site in T4 Lysozyme), conformational changes
	can make a difference of several kcal/mol in computed binding free
	energies, and that they are neglected in computed binding free energies
	if the system remains kinetically trapped in a particular metastable
	state on simulation timescales. We introduce a general "confine-and-release"
	framework for free energy calculations that accounts for these free
	energies of conformational change. We illustrate its use in this
	model system by demonstrating that an umbrella sampling protocol
	can obtain converged binding free energies that are independent of
	the starting protein structure and include these conformational change
	free energies.},
  doi = {10.1021/ct700032n},
  institution = {Department of Pharmaceutical Chemistry, University of California
	at San Francisco, San Francisco, CA 94158-2517.},
  owner = {emilio},
  pmid = {18843379},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1021/ct700032n}
}

@ARTICLE{Mobley2006,
  author = {David L Mobley and John D Chodera and Ken A Dill},
  title = {On the use of orientational restraints and symmetry corrections in
	alchemical free energy calculations.},
  journal = {J. Chem. Phys.},
  year = {2006},
  volume = {125},
  pages = {084902},
  number = {8},
  month = {Aug},
  abstract = {Alchemical free energy calculations are becoming a useful tool for
	calculating absolute binding free energies of small molecule ligands
	to proteins. Here, we find that the presence of multiple metastable
	ligand orientations can cause convergence problems when distance
	restraints alone are used. We demonstrate that the use of orientational
	restraints can greatly accelerate the convergence of these calculations.
	However, even with this acceleration, we find that sufficient sampling
	requires substantially longer simulations than are used in many published
	protocols. To further accelerate convergence, we introduce a new
	method of configuration space decomposition by orientation which
	reduces required simulation lengths by at least a factor of 5 in
	the cases examined. Our method is easily parallelizable, well suited
	for cases where a ligand cocrystal structure is not available, and
	can utilize initial orientations generated by docking packages.},
  doi = {10.1063/1.2221683},
  institution = {Department of Pharmaceutical Chemistry, University of California
	at San Francisco, San Francisco, CA 94143, USA. dmobley@gmail.com},
  keywords = {Biophysics; Catechols; Chemistry, Physical; Computer Simulation; Crystallization;
	Ligands; Models, Chemical; Models, Molecular; Models, Statistical;
	Models, Theoretical; Molecular Conformation; Phenol; Proteins; Software;
	Thermodynamics},
  owner = {emilio},
  pmid = {16965052},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1063/1.2221683}
}

@ARTICLE{Mobley:Dill:review:2009,
  author = {David L Mobley and Ken A Dill},
  title = {Binding of small-molecule ligands to proteins: "what you see" is
	not always "what you get".},
  journal = {Structure},
  year = {2009},
  volume = {17},
  pages = {489--498},
  number = {4},
  month = {Apr},
  abstract = {We review insights from computational studies of affinities of ligands
	binding to proteins. The power of structural biology is in translating
	knowledge of protein structures into insights about their forces,
	binding, and mechanisms. However, the complementary power of computer
	modeling is in showing "the rest of the story" (i.e., how motions
	and ensembles and alternative conformers and the entropies and forces
	that cannot be seen in single molecular structures also contribute
	to binding affinities). Upon binding to a protein, a ligand can bind
	in multiple orientations; the protein or ligand can be deformed by
	the binding event; waters, ions, or cofactors can have unexpected
	involvement; and conformational or solvation entropies can sometimes
	play large and otherwise unpredictable roles. Computer modeling is
	helping to elucidate these factors.},
  doi = {10.1016/j.str.2009.02.010},
  institution = {Department of Chemistry, University of New Orleans, New Orleans,
	LA 70148, USA. dmobley@gmail.com},
  keywords = {Binding Sites; Computational Biology; Computer Simulation; Ligands;
	Models, Theoretical; Protein Binding; Protein Conformation; Proteins;
	Thermodynamics; Water},
  owner = {emilio},
  pii = {S0969-2126(09)00092-6},
  pmid = {19368882},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1016/j.str.2009.02.010}
}

@ARTICLE{Mobley2007b,
  author = {David L Mobley and Elise Dumont and John D Chodera and Ken A Dill},
  title = {Comparison of charge models for fixed-charge force fields: small-molecule
	hydration free energies in explicit solvent.},
  journal = {J Phys Chem B},
  year = {2007},
  volume = {111},
  pages = {2242--2254},
  number = {9},
  month = {Mar},
  abstract = {In molecular simulations with fixed-charge force fields, the choice
	of partial atomic charges influences numerous computed physical properties,
	including binding free energies. Many molecular mechanics force fields
	specify how nonbonded parameters should be determined, but various
	choices are often available for how these charges are to be determined
	for arbitrary small molecules. Here, we compute hydration free energies
	for a set of 44 small, neutral molecules in two different explicit
	water models (TIP3P and TIP4P-Ew) to examine the influence of charge
	model on agreement with experiment. Using the AMBER GAFF force field
	for nonbonded parameters, we test several different methods for obtaining
	partial atomic charges, including two fast methods exploiting semiempirical
	quantum calculations and methods deriving charges from the electrostatic
	potentials computed with several different levels of ab initio quantum
	calculations with and without a continuum reaction field treatment
	of solvent. We find that the best charge sets give a root-mean-square
	error from experiment of roughly 1 kcal/mol. Surprisingly, agreement
	with experimental hydration free energies does not increase substantially
	with increasing level of quantum theory, even when the quantum calculations
	are performed with a reaction field treatment to better model the
	aqueous phase. We also find that the semiempirical AM1-BCC method
	for computing charges works almost as well as any of the more computationally
	expensive ab initio methods and that the root-mean-square error reported
	here is similar to that for implicit solvent models reported in the
	literature. Further, we find that the discrepancy with experimental
	hydration free energies grows substantially with the polarity of
	the compound, as does its variation across theory levels.},
  doi = {10.1021/jp0667442},
  institution = {Department of Pharmaceutical Chemistry and Graduate Group in Biophysics,
	University of California at San Francisco, San Francisco, California
	94143, USA. dmobley@maxwell.compbio.ucsf.edu},
  keywords = {Biophysics; Chemistry, Physical; Computer Simulation; Energy Transfer;
	Entropy; Models, Chemical; Models, Statistical; Molecular Conformation;
	Molecular Structure; Solvents; Static Electricity; Temperature; Thermodynamics;
	Water},
  owner = {emilio},
  pmid = {17291029},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1021/jp0667442}
}

@ARTICLE{Mobley2007a,
  author = {David L Mobley and Alan P Graves and John D Chodera and Andrea C
	McReynolds and Brian K Shoichet and Ken A Dill},
  title = {Predicting absolute ligand binding free energies to a simple model
	site.},
  journal = {J. Mol. Biol.},
  year = {2007},
  volume = {371},
  pages = {1118--1134},
  number = {4},
  month = {Aug},
  abstract = {A central challenge in structure-based ligand design is the accurate
	prediction of binding free energies. Here we apply alchemical free
	energy calculations in explicit solvent to predict ligand binding
	in a model cavity in T4 lysozyme. Even in this simple site, there
	are challenges. We made systematic improvements, beginning with single
	poses from docking, then including multiple poses, additional protein
	conformational changes, and using an improved charge model. Computed
	absolute binding free energies had an RMS error of 1.9 kcal/mol relative
	to previously determined experimental values. In blind prospective
	tests, the methods correctly discriminated between several true ligands
	and decoys in a set of putative binders identified by docking. In
	these prospective tests, the RMS error in predicted binding free
	energies relative to those subsequently determined experimentally
	was only 0.6 kcal/mol. X-ray crystal structures of the new ligands
	bound in the cavity corresponded closely to predictions from the
	free energy calculations, but sometimes differed from those predicted
	by docking. Finally, we examined the impact of holding the protein
	rigid, as in docking, with a view to learning how approximations
	made in docking affect accuracy and how they may be improved.},
  doi = {10.1016/j.jmb.2007.06.002},
  institution = {Department of Pharmaceutical Chemistry, University of California
	at San Francisco, San Francisco, CA 94143-2518, USA.},
  keywords = {Binding Sites; Computer Simulation; Crystallography, X-Ray; Hydrophobicity;
	Ligands; Models, Molecular; Protein Binding; Protein Structure, Tertiary;
	Proteins; Temperature; Titrimetry},
  owner = {emilio},
  pii = {S0022-2836(07)00776-0},
  pmid = {17599350},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1016/j.jmb.2007.06.002}
}

@ARTICLE{Mobley:Bayly:Dill:2009,
  author = {Mobley, {D. L.} and Bayly, {C. I.} and Cooper, {M. D.} and Shirts,
	{M. R.} and Dill, {K. A.}},
  title = {Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive
	Test of Fixed-Charge Atomistic Simulations},
  journal = {J. Chem. Theory Comput.},
  year = {2009},
  volume = {Web Article ASAP},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Mobley:Chodera:Dill:2008,
  author = {Mobley, {D. L.} and Chodera, {J. D.} and Dill, {K. A.}},
  title = {Entropy and conformational change in implicit solvent simulations
	of small molecules},
  journal = {J. Phys. Chem. B},
  year = {2008},
  volume = {112},
  pages = {938--946},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Moghaddam2009,
  author = {Sarvin Moghaddam and Yoshihisa Inoue and Michael K Gilson},
  title = {Host-guest complexes with protein-ligand-like affinities: computational
	analysis and design.},
  journal = {J Am Chem Soc},
  year = {2009},
  volume = {131},
  pages = {4012--4021},
  number = {11},
  month = {Mar},
  abstract = {It has recently been discovered that guests combining a nonpolar core
	with cationic substituents bind cucurbit[7]uril (CB[7]) in water
	with ultrahigh affinities. The present study uses the Mining Minima
	algorithm to study the physics of these extraordinary associations
	and to computationally test a new series of CB[7] ligands designed
	to bind with similarly high affinity. The calculations reproduce
	key experimental observations regarding the affinities of ferrocene-based
	guests with CB[7] and beta-cyclodextrin and provide a coherent view
	of the roles of electrostatics and configurational entropy as determinants
	of affinity in these systems. The newly designed series of compounds
	is based on a bicyclo[2.2.2]octane core, which is similar in size
	and polarity to the ferrocene core of the existing series. Mining
	Minima predicts that these new compounds will, like the ferrocenes,
	bind CB[7] with extremely high affinities.},
  doi = {10.1021/ja808175m},
  institution = {Center for Advanced Research in Biotechnology, University of Maryland
	Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland
	20850, USA.},
  keywords = {Algorithms; Bridged Compounds, chemistry; Cations; Entropy; Ferrous
	Compounds, chemistry; Imidazoles, chemistry; Ligands; Octanes; Proteins;
	Static Electricity; beta-Cyclodextrins},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {10.1021/ja808175m},
  pmid = {19133781},
  timestamp = {2011.06.29},
  url = {http://dx.doi.org/10.1021/ja808175m}
}

@ARTICLE{Moghaddam2011,
  author = {Sarvin Moghaddam and Cheng Yang and Mikhail Rekharsky and Young Ho
	Ko and Kimoon Kim and Yoshihisa Inoue and Michael K Gilson},
  title = {New ultrahigh affinity host-guest complexes of cucurbit[7]uril with
	bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis
	and evaluation of M2 affinity calculations.},
  journal = {J Am Chem Soc},
  year = {2011},
  volume = {133},
  pages = {3570--3581},
  number = {10},
  month = {Mar},
  abstract = {A dicationic ferrocene derivative has previously been shown to bind
	cucurbit[7]uril (CB[7]) in water with ultrahigh affinity (ΔG(o) =
	-21 kcal/mol). Here, we describe new compounds that bind aqueous
	CB[7] equally well, validating our prior suggestion that they, too,
	would be ultrahigh affinity CB[7] guests. The present guests, which
	are based upon either a bicyclo[2.2.2]octane or adamantane core,
	have no metal atoms, so these results also confirm that the remarkably
	high affinities of the ferrocene-based guest need not be attributed
	to metal-specific interactions. Because we used the M2 method to
	compute the affinities of several of the new host-guest systems prior
	to synthesizing them, the present results also provide for the first
	blinded evaluation of this computational method. The blinded calculations
	agree reasonably well with experiment and successfully reproduce
	the observation that the new adamantane-based guests achieve extremely
	high affinities, despite the fact that they position a cationic substituent
	at only one electronegative portal of the CB[7] host. However, there
	are also significant deviations from experiment, and these lead to
	the correction of a procedural error and an instructive evaluation
	of the sensitivity of the calculations to physically reasonable variations
	in molecular energy parameters. The new experimental and computational
	results presented here bear on the physical mechanisms of molecular
	recognition, the accuracy of the M2 method, and the usefulness of
	host-guest systems as test-beds for computational methods.},
  doi = {10.1021/ja109904u},
  institution = {Center for Advanced Research in Biotechnology, University of Maryland
	Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland
	20850, United States.},
  keywords = {Adamantane, chemistry; Bicyclo Compounds, Heterocyclic, chemistry;
	Bridged Compounds, chemistry; Imidazoles, chemistry; Mathematical
	Computing; Thermodynamics},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {21341773},
  timestamp = {2011.06.29},
  url = {http://dx.doi.org/10.1021/ja109904u}
}

@ARTICLE{Mongan:Simmerling:McCammon:Case:Onufriev:2007,
  author = {Mongan, J. and Simmerling, C. and McCammon, {J. A.} and Case, {D.
	A} and Onufriev, A.},
  title = {Generalized {B}orn model with a simple, robust molecular volume correction},
  journal = {J. Chem. Theory Comput.},
  year = {2007},
  volume = {3},
  pages = {156--169},
  owner = {emilio},
  timestamp = {2010.11.01}
}

@BOOK{Montellano2005,
  title = {Cytochrome P450 : structure, mechanism, and biochemistry},
  publisher = {Kluwer Academic/Plenum Publishers},
  year = {2005},
  author = {Paul R. Ortiz de Montellano},
  edition = {3rd},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Morgantini:Kollman:95,
  author = {Morgantini, P.-Y. and Kollman, P. A.},
  journal = {J. Am. Chem. Soc.},
  year = {1995},
  volume = {117},
  pages = {6057},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Morozov:Kortemme:2005,
  author = {Morozov, {A. V.} and Kortemme, T.},
  title = {Potential functions for hydrogen bonds in protein structure prediction
	and design},
  journal = {Adv. Prot. Chem.},
  year = {2005},
  volume = {72},
  pages = {1--38},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Morra2010,
  author = {Giulia Morra and Alessandro Genoni and Marco A C Neves and Kenneth
	M Merz and Giorgio Colombo},
  title = {Molecular recognition and drug-lead identification: what can molecular
	simulations tell us?},
  journal = {Curr Med Chem},
  year = {2010},
  volume = {17},
  pages = {25--41},
  number = {1},
  month = {Jan},
  abstract = {Molecular recognition and ligand binding involving proteins underlie
	the most important life processes within the cell, such as substrate
	transport, catalysis, signal transmission, receptor trafficking,
	gene regulation, switching on and off of biochemical pathways. Despite
	recent successes in predicting the structures of many protein-substrate
	complexes, the dynamic aspects of binding have been largely neglected
	by computational/theoretical investigations. Recently, several groups
	have started tackling these problems with the use of experimental
	and simulation methods and developed models describing the variation
	of protein dynamics upon complex formation, shedding light on how
	substrate or inhibitor binding can alter protein flexibility and
	function. The study of ligand-induced dynamic variations has also
	been exploited to review the concept of allosteric changes, in the
	absence of major conformational changes. In this context, the study
	of the influence of protein motions on signal transduction and on
	catalytic activities has been used to develop pharmacophore models
	based on ensembles of protein conformations. These models, taking
	flexibility explicitly into account, are able to distinguish active
	inhibitors versus nonactive drug-like compounds, to define new molecular
	motifs and to preferentially identify specific ligands for a certain
	protein target. The application of these methods holds great promise
	in advancing structure-based drug discovery and medicinal chemistry
	in general, opening up the possibility to explore broader chemical
	spaces than is normally done in an efficient way. In this review,
	examples illustrating the extent to which simulations can be used
	to understand these phenomena will be presented along with examples
	of methodological developments to increase physical understanding
	of the processes and improve the possibility to rationally design
	new molecules.},
  institution = {Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale
	delle Ricerche, Via Mario Bianco 19, Milan, Italy.},
  owner = {emilio},
  pii = {CMC - AbsEpub/2010 - 003},
  pmid = {19941480},
  review = {Maybe useful for curr. op. review. Asked library for reprint.},
  timestamp = {2010.06.07}
}

@ARTICLE{Morton1995,
  author = {A. Morton and W. A. Baase and B. W. Matthews},
  title = {Energetic origins of specificity of ligand binding in an interior
	nonpolar cavity of T4 lysozyme.},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {8564--8575},
  number = {27},
  month = {Jul},
  abstract = {To determine the constraints on interactions within the core of a
	folded protein, we have analyzed the binding of 91 different compounds
	to an internal cavity created in the interior of phage T4 lysozyme
	by site-directed mutagenesis [Eriksson et al. (1992a) Nature 355,
	371-373]. The cavity is able to accommodate a variety of small, mainly
	nonpolar, ligands. Molecules which do not appear to bind include
	those that are very polar, those that are too large, and those that
	have appropriate volume and polarity but inappropriate shape. Calorimetric
	analysis of 16 of these ligands reveals that their free energies
	of binding are poorly correlated with their solvent-transfer free
	energies. In addition, their enthalpies of binding are much larger
	than expected on the basis of transfer of the ligands from an aqueous
	to a nonpolar liquid phase. The binding energetics were analyzed
	by dividing the reaction into three processes: desolvation, immobilization,
	and packing. This analysis indicates that all three processes contribute
	to binding specificity. For a subset of these ligands that are structurally
	related, however, packing interactions in the protein interior are
	well modeled by the interactions of the ligands with octanol.},
  institution = {Institute of Molecular Biology, Howard Hughes Medical Institute,
	Eugene, Oregon, USA.},
  keywords = {Bacteriophage T4; Calorimetry; Ligands; Muramidase; Protein Binding;
	Substrate Specificity; Thermodynamics},
  owner = {emilio},
  pmid = {7612598},
  timestamp = {2010.04.27}
}

@ARTICLE{Morton1995a,
  author = {A. Morton and B. W. Matthews},
  title = {Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme:
	linkage of dynamics and structural plasticity.},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {8576--8588},
  number = {27},
  month = {Jul},
  abstract = {To better understand the role of shape complementarity in ligand binding
	and protein core interactions, the structures have been determined
	of a set of ligands bound within a cavity-containing mutant of T4
	lysozyme. The interior cavity is seen to consist of two parts that
	respond very differently to the binding of ligands. First, there
	is a relatively rigid region that does not relax significantly upon
	binding any ligand. Second, there is a more flexible region that
	moves to various extents in response to binding the different ligands.
	The part of the binding site that remains rigid is characterized
	by low temperature factors and strong protection from hydrogen exchange.
	This part of the site appears to be primarily responsible for discriminating
	between ligands of different shape (i.e., for determining specificity).
	The more flexible region, characterized by relatively high temperature
	factors and weak protection from hydrogen exchange, allows some promiscuity
	in binding by undergoing variable amounts of deformation at essentially
	the same energetic cost. This linkage between the dynamic information
	represented by crystallographic temperature factors and hydrogen-exchange
	behavior on the one hand, and structural plasticity in response to
	ligand binding on the other hand, suggests a way to improve our understanding
	of steric interactions in protein cores and protein-ligand binding
	sites. Ligand design and packing algorithms might take advantage
	of this information, requiring complementary interactions where the
	protein is rigid and allowing some overlap in regions where the protein
	is flexible.},
  institution = {Institute of Molecular Biology, Howard Hughes Medical Institute,
	Eugene, Oregon, USA.},
  keywords = {Bacteriophage T4; Benzene Derivatives; Benzofurans; Computer Graphics;
	Crystallography, X-Ray; Hydrogen Bonding; Indenes; Indoles; Ligands;
	Models, Molecular; Muramidase; Protein Binding; Protein Conformation;
	Xylenes},
  owner = {emilio},
  pmid = {7612599},
  timestamp = {2010.04.30}
}

@ARTICLE{Moult2009,
  author = {John Moult and Krzysztof Fidelis and Andriy Kryshtafovych and Burkhard
	Rost and Anna Tramontano},
  title = {Critical assessment of methods of protein structure prediction -
	Round VIII.},
  journal = {Proteins},
  year = {2009},
  volume = {77 Suppl 9},
  pages = {1--4},
  abstract = {This article is an introduction to the special issue of the journal
	Proteins, dedicated to the eighth CASP experiment to assess the state
	of the art in protein structure prediction. The article describes
	the conduct of the experiment, the categories of prediction included,
	and outlines the evaluation and assessment procedures. Highlights
	are the first blind assessment of model refinement methods showing
	that under some circumstances substantial model improvements are
	possible; improvements in the performance of methods for determining
	the accuracy of a model; and some progress in the accuracy of comparative
	models in regions not present in a principal template. Against these
	advances must be stacked the fact that there is no detectable progress
	in model quality compared with CASP7 in either template-based or
	template free modeling, using the established CASP measures.},
  doi = {10.1002/prot.22589},
  institution = {Center for Advanced Research in Biotechnology, University of Maryland
	Biotechnology Institute, Rockville, Maryland 20850, USA. moult@umbi.umd.edu},
  keywords = {Computational Biology, methods; Models, Molecular; Protein Conformation;
	Proteins, chemistry; Sequence Analysis, Protein, methods},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {19774620},
  timestamp = {2011.10.15},
  url = {http://dx.doi.org/10.1002/prot.22589}
}

@ARTICLE{Mountain:Thirumalai:98,
  author = {Mountain, R. D. and Thirumalai, D.},
  title = {Hydration for a Series of Hydrocarbons},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1998},
  volume = {95},
  pages = {8436-40},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Muddana:Gilson:2012,
  author = {Hari S. Muddana and C. Daniel Varnado and Christopher W. Bielawski
	and Adam R. Urbach and Lyle Isaacs and Matthew T. Geballe and Michael
	K. Gilson},
  title = {Blind prediction of host-guest binding affinities: A new SAMPL3 challenge},
  journal = {J. Comp. Aided Mol. Design},
  year = {2012},
  volume = {Online First},
  pages = {1--13},
  owner = {emilio},
  timestamp = {2012.02.09}
}

@ARTICLE{Muegge:97,
  author = {Muegge, I. and Qi, P. Wand, A. J. and Chu, Z. and Warshel, A.},
  journal = {J. Phys. Chem.},
  year = {1997},
  volume = {101},
  pages = {825-836},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Murata2004,
  author = {Murata, Katsumi and Sugita, Yuji and Okamoto, Yuko},
  title = {Free energy calculations for DNA base stacking by replica-exchange
	umbrella sampling},
  journal = {Chemical Physics Letters},
  year = {2004},
  volume = {385},
  pages = {1--7},
  number = {1-2},
  month = feb,
  abstract = {We have investigated the free energy change of the stacking process
	of DNA dimers using molecular dynamics simulations based on replica-exchange
	umbrella sampling. Pairs of replicas with different umbrella potentials
	are exchanged in this method, which allows the simulation to sample
	much wider conformational space and, therefore, to yield more accurate
	free energy profiles than by the conventional umbrella sampling.
	From the free energy profiles, we observed good stacking for all
	DNA dimers and sequence-dependent stacking stability. This sequence
	dependence of the stacking free energy is in accord with the experimental
	results.},
  issn = {0009-2614},
  owner = {emilio},
  timestamp = {2011.01.13},
  url = {http://www.sciencedirect.com/science/article/B6TFN-4BF0FS8-1/2/461168ed104e0a27763399c7b68e8575}
}

@ARTICLE{Naim2007,
  author = {Marwen Naim and Sathesh Bhat and Kathryn N Rankin and Sheldon Dennis
	and Shafinaz F Chowdhury and Imran Siddiqi and Piotr Drabik and Traian
	Sulea and Christopher I Bayly and Araz Jakalian and Enrico O Purisima},
  title = {Solvated interaction energy (SIE) for scoring protein-ligand binding
	affinities. 1. Exploring the parameter space.},
  journal = {J. Chem. Inf. Model.},
  year = {2007},
  volume = {47},
  pages = {122--133},
  number = {1},
  abstract = {We present a binding free energy function that consists of force field
	terms supplemented by solvation terms. We used this function to calibrate
	the solvation model along with the binding interaction terms in a
	self-consistent manner. The motivation for this approach was that
	the solute dielectric-constant dependence of calculated hydration
	gas-to-water transfer free energies is markedly different from that
	of binding free energies (J. Comput. Chem. 2003, 24, 954). Hence,
	we sought to calibrate directly the solvation terms in the context
	of a binding calculation. The five parameters of the model were systematically
	scanned to best reproduce the absolute binding free energies for
	a set of 99 protein-ligand complexes. We obtained a mean unsigned
	error of 1.29 kcal/mol for the predicted absolute binding affinity
	in a parameter space that was fairly shallow near the optimum. The
	lowest errors were obtained with solute dielectric values of Din
	= 20 or higher and scaling of the intermolecular van der Waals interaction
	energy by factors ranging from 0.03 to 0.15. The high apparent Din
	and strong van der Waals scaling may reflect the anticorrelation
	of the change in solvated potential energy and configurational entropy,
	that is, enthalpy-entropy compensation in ligand binding (Biophys.
	J. 2004, 87, 3035-3049). Five variations of preparing the protein-ligand
	data set were explored in order to examine the effect of energy refinement
	and the presence of bound water on the calculated results. We find
	that retaining water in the final protein structure used for calculating
	the binding free energy is not necessary to obtain good results;
	that is the continuum solvation model is sufficient. Virtual screening
	enrichment studies on estrogen receptor and thymidine kinase showed
	a good ability of the binding free energy function to recover true
	hits in a collection of decoys.},
  doi = {10.1021/ci600406v},
  institution = {Biotechnology Research Institute, National Research Council of Canada,
	6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2.},
  keywords = {Ligands; Models, Chemical; Protein Binding; Proteins; Solubility;
	Thermodynamics},
  owner = {emilio},
  pmid = {17238257},
  timestamp = {2010.05.20},
  url = {http://dx.doi.org/10.1021/ci600406v}
}

@ARTICLE{Neale2008,
  author = {Neale, Chris and Rodinger, Tomas and Pom\`{e}s, R\'{e}gis},
  title = {Equilibrium exchange enhances the convergence rate of umbrella sampling},
  journal = {Chemical Physics Letters},
  year = {2008},
  volume = {460},
  pages = {375--381},
  number = {1-3},
  month = jul,
  abstract = {Umbrella sampling, a technique for sampling energetically unfavorable
	states by computer simulation, is subject to systematic sampling
	errors arising from quasi-nonergodicity. In order to address this
	problem, we compare free energy profiles generated along the backbone
	dihedral angles [phi] and [psi] of alanine dipeptide in water using
	umbrella sampling successively with and without the provision of
	equilibrium exchange between umbrellas. The results show that the
	addition of equilibrium exchange to umbrella sampling alleviates
	these errors by restoring the utilization of transition paths that
	leave and reenter the specified sampling region.},
  issn = {0009-2614},
  owner = {emilio},
  timestamp = {2011.01.13},
  url = {http://www.sciencedirect.com/science/article/B6TFN-4SNWW5G-4/2/98da66b857baba6946547f2f077e392b}
}

@ARTICLE{Sheraga:62,
  author = {Nemethy, G. and Sheraga, H. A.},
  journal = {J. Chem. Phys.},
  year = {1962},
  volume = {36},
  pages = {3401},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Neumann:85,
  author = {Neumann, M.},
  journal = {J. Chem. Phys.},
  year = {1985},
  volume = {82},
  pages = {5663-5670},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{New:Berne:95,
  author = {New, M. H. and Berne, B. J.},
  title = {Molecular Dynamics Calculation of the Effect of Solvent Polarizability
	on the Hydrophobic Interaction},
  journal = {J. Am. Chem. Soc.},
  year = {1995},
  volume = {117},
  pages = {7172-7179},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Newman2009,
  author = {Janet Newman and Vincent J Fazio and Tom T Caradoc-Davies and Kim
	Branson and Thomas S Peat},
  title = {Practical aspects of the SAMPL challenge: providing an extensive
	experimental data set for the modeling community.},
  journal = {J. Biomol. Screen.},
  year = {2009},
  volume = {14},
  pages = {1245--1250},
  number = {10},
  month = {Dec},
  abstract = {To provide an experimental basis for a comprehensive molecular modeling
	evaluation study, 500 fragments from the Maybridge fragment library
	were soaked into crystals of bovine pancreatic trypsin and the structures
	determined by X-ray crystallography. The soaking experiments were
	performed in both single and pooled aliquots to determine if combination
	of fragments is an appropriate strategy. A further set of data was
	obtained from co-crystallizing the pooled fragments with the protein.
	X-ray diffraction data were collected on approximately 1000 crystals
	at the Australian Synchrotron, and these data were subsequently processed,
	and the preliminary analysis was performed with a custom software
	application (Jigsaw), which combines available software packages
	for structure solution and analysis.},
  doi = {10.1177/1087057109348220},
  institution = {CSIRO Molecular and Health Technologies, Parkville, VIC, 3052 Australia.},
  keywords = {Animals; Benzylamines; Calcium Chloride; Cattle; Crystallization;
	Databases, Protein; Models, Molecular; Models, Statistical; Software;
	Trypsin},
  owner = {emilio},
  pii = {1087057109348220},
  pmid = {19822883},
  timestamp = {2010.10.27},
  url = {http://dx.doi.org/10.1177/1087057109348220}
}

@BOOK{NewmanBook19

repository: radical-papers/radical-references

repo_name: radical-papers/radical-references