text:
99,
  title = {Monte Carlo Methods in Statistical Physics},
  publisher = {Oxford University Press. New York},
  year = {1999},
  author = {Newman, M. E. J. and Barkema, G. T.},
  comment = {From Zhiqiang},
  owner = {emilio},
  timestamp = {2011.11.06}
}

@ELECTRONIC{Nguyen:Gilson:Young:2011,
  author = {Crystal Nguyen and Michael K. Gilson and Tom Young},
  year = {2011},
  title = {Structure and Thermodynamics of Molecular Hydration via Grid Inhomogeneous
	Solvation Theory},
  howpublished = {arXiv:1108.4876v1 [q-bio.BM]},
  owner = {emilio},
  timestamp = {2012.02.09}
}

@ARTICLE{Nicholls2010,
  author = {Anthony Nicholls and Georgia B McGaughey and Robert P Sheridan and
	Andrew C Good and Gregory Warren and Magali Mathieu and Steven W
	Muchmore and Scott P Brown and J. Andrew Grant and James A Haigh
	and Neysa Nevins and Ajay N Jain and Brian Kelley},
  title = {Molecular Shape and Medicinal Chemistry: A Perspective.},
  journal = {J Med Chem},
  year = {2010},
  month = {Feb},
  doi = {10.1021/jm900818s},
  institution = {ta Fe, New Mexico 87508.},
  owner = {emilio},
  pmid = {20158188},
  timestamp = {2010.05.01},
  url = {http://dx.doi.org/10.1021/jm900818s}
}

@ARTICLE{Nicholls1991,
  author = {Nicholls, A. and Sharp, K. A. and Honig, B.},
  title = {Protein folding and association: insights from the interfacial and
	thermodynamic properties of hydrocarbons},
  journal = {Proteins},
  year = {1991},
  volume = {11},
  pages = {281-96},
  number = {4},
  abstract = {We demonstrate in this work that the surface tension, water-organic
	solvent, transfer-free energies and the thermodynamics of melting
	of linear alkanes provide fundamental insights into the nonpolar
	driving forces for protein folding and protein binding reactions.
	We first develop a model for the curvature dependence of the hydrophobic
	effect and find that the macroscopic concept of interfacial free
	energy is applicable at the molecular level. Application of a well-known
	relationship involving surface tension and adhesion energies reveals
	that dispersion forces play little or no net role in hydrophobic
	interactions; rather, the standard model of disruption of water structure
	(entropically driven at 25 degrees C) is correct. The hydrophobic
	interaction is found, in agreement with the classical picture, to
	provide a major driving force for protein folding. Analysis of the
	melting behavior of hydrocarbons reveals that close packing of the
	protein interior makes only a small free energy contribution to folding
	because the enthalpic gain resulting from increased dispersion interactions
	(relative to the liquid) is countered by the freezing of side chain
	motion. The identical effect should occur in association reactions,
	which may provide an enormous simplification in the evaluation of
	binding energies. Protein binding reactions, even between nearly
	planar or concave/convex interfaces, are found to have effective
	hydrophobicities considerably smaller than the prediction based on
	macroscopic surface tension. This is due to the formation of a concave
	collar region that usually accompanies complex formation. This effect
	may preclude the formation of complexes between convex surfaces.},
  address = {Department of Biochemistry and Molecular Biophysics, Columbia University,
	New York, New York 10032.},
  comment = {Protein folding and association: insights from the interfacial and
	thermodynamic properties of hydrocarbons

	1758883

	Nicholls, A Sharp, K A Honig, B GM 41371/GM/NIGMS NIH HHS/United States
	GM-30518/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov't,
	Non-P.H.S. Research Support, U.S. Gov't, P.H.S. United states Proteins
	Proteins. 1991;11(4):281-96.

	eng},
  issn = {0887-3585 (Print) 0887-3585 (Linking)},
  keywords = {Algorithms Hydrocarbons/*chemistry *Protein Binding *Protein Conformation
	Surface Tension Thermodynamics},
  owner = {mauro},
  refid = {49},
  timestamp = {2011.07.22},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1758883}
}

@ARTICLE{Nielsen2011,
  author = {Nielsen, Jens E. and Gunner, M. R. and Garc\'{i}a-Moreno E., Bertrand},
  title = {The pKa Cooperative: A collaborative effort to advance structure-based
	calculations of pKa values and electrostatic effects in proteins},
  journal = {Proteins},
  year = {2011},
  volume = {79},
  pages = {3249--3259},
  number = {12},
  abstract = {The pKa Cooperative (http://www.pkacoop.org) was organized to advance
	development of accurate and useful computational methods for structure-based
	calculation of pKa values and electrostatic energies in proteins.
	The Cooperative brings together laboratories with expertise and interest
	in theoretical, computational, and experimental studies of protein
	electrostatics. To improve structure-based energy calculations, it
	is necessary to better understand the physical character and molecular
	determinants of electrostatic effects. Thus, the Cooperative intends
	to foment experimental research into fundamental aspects of proteins
	that depend on electrostatic interactions. It will maintain a depository
	for experimental data useful for critical assessment of methods for
	structure-based electrostatics calculations. To help guide the development
	of computational methods, the Cooperative will organize blind prediction
	exercises. As a first step, computational laboratories were invited
	to reproduce an unpublished set of experimental pKa values of acidic
	and basic residues introduced in the interior of staphylococcal nuclease
	by site-directed mutagenesis. The pKa values of these groups are
	unique and challenging to simulate owing to the large magnitude of
	their shifts relative to normal pKa values in water. Many computational
	methods were tested in this first Blind Prediction Challenge and
	critical assessment exercise. A workshop was organized in the Telluride
	Science Research Center to objectively assess the performance of
	many computational methods tested on this one extensive data set.
	This volume of Proteins: Structure, Function, and Bioinformatics
	introduces the pKa Cooperative, presents reports submitted by participants
	in the Blind Prediction Challenge, and highlights some of the problems
	in structure-based calculations identified during this exercise.
	Proteins 2011; © 2011 Wiley-Liss, Inc.},
  issn = {1097-0134},
  keywords = {proteins, pKa values, electrostatics, pH, ionizable, staphylococcal
	nuclease, simulation},
  owner = {emilio},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  timestamp = {2012.02.09},
  url = {http://dx.doi.org/10.1002/prot.23194}
}

@ARTICLE{Nina:Beglov:Roux:97,
  author = {Nina, M. and Beglov, D. and Roux, B.},
  title = {Atomic Radii for Continuum Electrostatic Calculations Based on Molecular
	Dynamics Free Energy Simulations},
  journal = {J. Phys. Chem. B},
  year = {1997},
  volume = {101},
  pages = {5239-5248},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Noe2009,
  author = {Frank No\'{e} and Christof Schutte and Eric Vanden-Eijnden and Lothar
	Reich and Thomas R Weikl},
  title = {Constructing the equilibrium ensemble of folding pathways from short
	off-equilibrium simulations.},
  journal = {Proc Natl Acad Sci U S A},
  year = {2009},
  volume = {106},
  pages = {19011--19016},
  number = {45},
  month = {Nov},
  abstract = {Characterizing the equilibrium ensemble of folding pathways, including
	their relative probability, is one of the major challenges in protein
	folding theory today. Although this information is in principle accessible
	via all-atom molecular dynamics simulations, it is difficult to compute
	in practice because protein folding is a rare event and the affordable
	simulation length is typically not sufficient to observe an appreciable
	number of folding events, unless very simplified protein models are
	used. Here we present an approach that allows for the reconstruction
	of the full ensemble of folding pathways from simulations that are
	much shorter than the folding time. This approach can be applied
	to all-atom protein simulations in explicit solvent. It does not
	use a predefined reaction coordinate but is based on partitioning
	the state space into small conformational states and constructing
	a Markov model between them. A theory is presented that allows for
	the extraction of the full ensemble of transition pathways from the
	unfolded to the folded configurations. The approach is applied to
	the folding of a PinWW domain in explicit solvent where the folding
	time is two orders of magnitude larger than the length of individual
	simulations. The results are in good agreement with kinetic experimental
	data and give detailed insights about the nature of the folding process
	which is shown to be surprisingly complex and parallel. The analysis
	reveals the existence of misfolded trap states outside the network
	of efficient folding intermediates that significantly reduce the
	folding speed.},
  doi = {10.1073/pnas.0905466106},
  institution = {Deutsche Forschungsgemeinschaft Research Center Matheon, Freie Universität
	Berlin, Arnimallee 6, 14195 Berlin, Germany. frank.noe@fu-berlin.de},
  keywords = {Computational Biology; Computer Simulation; Models, Chemical; Protein
	Conformation; Protein Folding; Proteins},
  owner = {emilio},
  pii = {0905466106},
  pmid = {19887634},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1073/pnas.0905466106}
}

@BOOK{NocedalBook1999,
  title = {Numerical Optimization},
  publisher = {Springer-Verlag, New York},
  year = {1999},
  author = {Nocedal, J. and Wright, S. J.},
  comment = {From Zhiqiang},
  owner = {emilio},
  timestamp = {2011.11.06}
}

@ARTICLE{Nose:1984,
  author = {Nos\`{e}, S.},
  title = {A unified formulation of the constant temperature molecular dynamics
	methods},
  journal = {J. Chem. Phys.},
  year = {1984},
  volume = {81},
  pages = {511-519},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Novotny:Bruccoleri:Davis:Sharp:97,
  author = {Novotny, J. and Bruccoleri, R. E. and Davis, D. and Sharp, K. A},
  title = {Empirical free energy calculations: a blind test and further improvements
	of the method},
  journal = {J. Mol. Biol.},
  year = {1997},
  volume = {268},
  pages = {401-411},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Noe2008,
  author = {Frank Noé and Stefan Fischer},
  title = {Transition networks for modeling the kinetics of conformational change
	in macromolecules.},
  journal = {Curr Opin Struct Biol},
  year = {2008},
  volume = {18},
  pages = {154--162},
  number = {2},
  month = {Apr},
  abstract = {The kinetics and thermodynamics of complex transitions in biomolecules
	can be modeled in terms of a network of transitions between the relevant
	conformational substates. Such a transition network, which overcomes
	the fundamental limitations of reaction-coordinate-based methods,
	can be constructed either based on the features of the energy landscape,
	or from molecular dynamics simulations. Energy-landscape-based networks
	are generated with the aid of automated path-optimization methods,
	and, using graph-theoretical adaptive methods, can now be constructed
	for large molecules such as proteins. Dynamics-based networks, also
	called Markov State Models, can be interpreted and adaptively improved
	using statistical concepts, such as the mean first passage time,
	reactive flux and sampling error analysis. This makes transition
	networks powerful tools for understanding large-scale conformational
	changes.},
  doi = {10.1016/j.sbi.2008.01.008},
  institution = {Research Center "Matheon", FU Berlin, Arnimallee 6, 14195 Berlin,
	Germany. noe@math.fu-berlin.de},
  keywords = {Kinetics; Macromolecular Substances; Models, Chemical; Molecular Conformation;
	Proteins; Thermodynamics},
  owner = {emilio},
  pii = {S0959-440X(08)00024-9},
  pmid = {18378442},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1016/j.sbi.2008.01.008}
}

@ARTICLE{Nymeyer:Gnanakaran:Garcia:2004,
  author = {Nymeyer, H. and Gnanakaran, S. and Garcia, {A. E.}},
  title = {Atomic Simulations of Protein Folding Using the Replica Exchange
	Algorithm},
  journal = {Methods in Enzymology},
  year = {2004},
  volume = {383},
  pages = {119-149},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Okamoto2004,
  author = {Yuko Okamoto},
  title = {Generalized-ensemble algorithms: enhanced sampling techniques for
	Monte Carlo and molecular dynamics simulations.},
  journal = {J Mol Graph Model},
  year = {2004},
  volume = {22},
  pages = {425--439},
  number = {5},
  month = {May},
  abstract = {In complex systems with many degrees of freedom such as spin glass
	and biomolecular systems, conventional simulations in canonical ensemble
	suffer from the quasi-ergodicity problem. A simulation in generalized
	ensemble performs a random walk in potential energy space and overcomes
	this difficulty. From only one simulation run, one can obtain canonical
	ensemble averages of physical quantities as functions of temperature
	by the single-histogram and/or multiple-histogram reweighting techniques.
	In this article we review the generalized ensemble algorithms. Three
	well-known methods, namely, multicanonical algorithm (MUCA), simulated
	tempering (ST), and replica-exchange method (REM), are described
	first. Both Monte Carlo (MC) and molecular dynamics (MD) versions
	of the algorithms are given. We then present five new generalized-ensemble
	algorithms which are extensions of the above methods.},
  doi = {10.1016/j.jmgm.2003.12.009},
  institution = {Department of Theoretical Studies, Institute for Molecular Science,
	Okazaki, Aichi, Japan. okamotoy@ims.ac.jp},
  keywords = {Algorithms; Computer Simulation; Models, Molecular; Monte Carlo Method;
	Thermodynamics},
  owner = {emilio},
  pii = {S1093-3263(03)00198-0},
  pmid = {15099838},
  timestamp = {2011.03.07},
  url = {http://dx.doi.org/10.1016/j.jmgm.2003.12.009}
}

@ARTICLE{Okumura2010,
  author = {Hisashi Okumura and Emilio Gallicchio and Ronald M Levy},
  title = {Conformational populations of ligand-sized molecules by replica exchange
	molecular dynamics and temperature reweighting.},
  journal = {J. Comput. Chem.},
  year = {2010},
  volume = {31},
  pages = {1357--1367},
  abstract = {The use of the replica exchange (RE) molecular dynamics (MD) method
	for the efficient estimation of conformational populations of ligand-sized
	molecules in solution is investigated. We compare the computational
	efficiency of the traditional constant temperature MD technique with
	that of the parallel RE molecular dynamics method for a series of
	alkanes and rilpivirine (TMC278), an inhibitor against HIV-1 reverse
	transcriptase, with implicit solvation. We show that conformational
	populations are accurately estimated by both methods; however, replica
	exchange estimates converge at a faster rate, especially for rilpivirine,
	which is characterized by multiple stable states separated by high-free
	energy barriers. Furthermore, convergence is enhanced when the weighted
	histogram analysis method (WHAM) is used to estimate populations
	from the data collected from multiple RE temperature replicas. For
	small drug-like molecules with energetic barriers separating the
	stable states, the use of RE with WHAM is an efficient computational
	approach for estimating the contribution of ligand conformational
	reorganization to binding affinities.},
  comment = {Ligand reorganization},
  doi = {10.1002/jcc.21419},
  institution = {Department of Chemistry and Chemical Biology and BioMaPS Institute
	for Quantitative Biology, Rutgers University, Piscataway, New Jersey
	08854, USA. hokumura@ims.ac.jp},
  owner = {emilio},
  pmid = {19882731},
  timestamp = {2010.04.19},
  url = {http://dx.doi.org/10.1002/jcc.21419}
}

@ARTICLE{Okur:Wickstrom:Simmerling:2008,
  author = {Okur, A. and Wickstrom, L. and Simmerling, C.},
  title = {Evaluation of Salt Bridge Structure and Energetics in Peptides Using
	Explicit, Implicit, and Hybrid Solvation Models},
  journal = {J. Chem. Theory Comput.},
  year = {2008},
  volume = {4},
  pages = {488--498},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Olivieri2011,
  author = {Olivieri, Lilian and Gardebien, Fabrice},
  title = {Molecular Dynamics Simulations of a Binding Intermediate between
	FKBP12 and a High-Affinity Ligand},
  journal = {J. Chem. Theory Comput.},
  year = {2011},
  volume = {7},
  pages = {725--741},
  number = {3},
  abstract = {null},
  comment = {Molecular Dynamics Simulations of a Binding Intermediate between FKBP12
	and a High-Affinity Ligand

	doi: 10.1021/ct100394d},
  issn = {1549-9618},
  owner = {mauro},
  refid = {57},
  timestamp = {2011.07.22},
  url = {http://dx.doi.org/10.1021/ct100394d}
}

@ARTICLE{Onufriev:2008,
  author = {Onufriev, A.},
  title = {Implicit Solvent Models in Molecular Dynamics Simulations},
  journal = {Annual Reports in Computational Chemistry},
  year = {2008},
  volume = {4},
  pages = {125-137},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Onufriev:Bashford:Case:2000,
  author = {Onufriev, A. and Bashford, D. and Case, D. A.},
  title = {Modification of the Generalized Born Model Suitable for Macromolecules},
  journal = {J. Phys. Chem. B},
  year = {2000},
  volume = {104},
  pages = {3712-3720},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Onufriev:Bashford:Case:2004,
  author = {Onufriev, A. and Bashford, D. and Case, {D. A.}},
  title = {Exploring protein native states and large-scale conformational changes
	with a modified generalized born model},
  journal = {Proteins},
  year = {2004},
  volume = {55},
  pages = {383--394},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Onufriev:Case:Bashford:2002,
  author = {Onufriev, A. and Case, D. A. and Bashford, D.},
  title = {Effective Born Radii in the Generalized Born Approximation: The Importance
	of being perfect},
  journal = {J. Comp. Chem.},
  year = {2002},
  volume = {23},
  pages = {1297-1304},
  owner = {emilio},
  timestamp = {2010.11.01}
}

@ARTICLE{Ooi:Oobatake:Nemethy:Scheraga:87,
  author = {Ooi, T. and Oobatake, M. and Nemethy, G. and Sheraga, {H. A.}},
  title = {Accessible Surface Areas as a Measure of the Thermodynamic Parameters
	of Hydration of Pepetides},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1987},
  volume = {84},
  pages = {3086-3090},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Oostenbrink2000,
  author = {B. C. Oostenbrink and J. W. Pitera and van Lipzig MM and J. H. Meerman
	and van Gunsteren WF},
  title = {Simulations of the estrogen receptor ligand-binding domain: affinity
	of natural ligands and xenoestrogens.},
  journal = {J. Med. Chem.},
  year = {2000},
  volume = {43},
  pages = {4594--4605},
  number = {24},
  month = {Nov},
  abstract = {We have carried out molecular dynamics (MD) simulations and free energy
	calculations on the alpha-subtype of the human estrogen receptor
	ligand-binding domain (ERalpha LBD) complexed with a number of known
	agonists and putative xenoestrogens. Our dynamical simulations of
	ligand-receptor complexes underscore the highly structured nature
	of the complex and offer some interesting insights into the structure-activity
	relationship (SAR) for these ligands. With traditional thermodynamic
	integration (TI) calculations, we calculate relative binding free
	energies for three known agonists, in good agreement with experimental
	values. The sheer number of possible xenoestrogenic compounds makes
	an approach using traditional free energy calculations unfeasible.
	Instead, we have made use of a single-step perturbation methodology
	that allows the calculation of relative free energies for a large
	number of related polyaromatic hydrocarbons (PAHs) from a single
	simulation. Our results show good (maximum deviation 3.3 kJ mol(-1))
	agreement with experimental data, suggesting the possibility of large-scale
	xenoestrogen screening in silico to obtain strongly estrogenic compounds
	for subsequent experimental testing.},
  institution = {Division of Chemistry, Department of Pharmacochemistry, Section Molecular
	Toxicology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.},
  keywords = {Diethylstilbestrol; Estradiol; Estradiol Congeners; Estrogens; Genistein;
	Humans; Ligands; Models, Molecular; Polycyclic Hydrocarbons, Aro;
	Protein Structure, Secondary; Protein Structure, Tertiary; Receptors,
	Estrogen; Thermodynamics; Xenobiotics; matic},
  owner = {emilio},
  pii = {jm001045d},
  pmid = {11101351},
  timestamp = {2010.06.02}
}

@ARTICLE{Oostenbrink2005,
  author = {Chris Oostenbrink and Wilfred F van Gunsteren},
  title = {Free energies of ligand binding for structurally diverse compounds.},
  journal = {Proc. Natl. Acad Sci. USA},
  year = {2005},
  volume = {102},
  pages = {6750--6754},
  number = {19},
  month = {May},
  abstract = {The one-step perturbation approach is an efficient means to calculate
	many relative free energies from a common reference compound. Combining
	lessons learned in previous studies, an application of the method
	is presented that allows for the calculation of relative binding
	free energies for structurally rather diverse compounds from only
	a few simulations. Based on the well known statistical-mechanical
	perturbation formula, the results do not require any empirical parameters,
	or training sets, only limited knowledge of the binding characteristics
	of the ligands suffices to design appropriate reference compounds.
	Depending on the choice of reference compound, relative free energies
	of binding rigid ligands to the ligand-binding domain of the estrogen
	receptor can be obtained that show good agreement with the experimental
	values. The approach presented here can easily be applied to many
	rigid ligands, and it should be relatively easy to extend the method
	to account for ligand flexibility. The free-energy calculations can
	be straightforwardly parallelized, allowing for an efficient means
	to understand and predict relative binding free energies.},
  doi = {10.1073/pnas.0407404102},
  institution = {Laboratory of Physical Chemistry, Swiss Federal Institute of Technology,
	Eidgenössische Technische Hochschule-Hönggerberg, CH-8093 Zurich,
	Switzerland.},
  keywords = {Algorithms; Animals; Binding Sites; Estradiol Congeners, chemistry;
	Estradiol, chemistry; Ligands; Models, Chemical; Models, Molecular;
	Protein Binding; Protein Conformation; Protein Structure, Tertiary;
	Proteins, chemistry; Receptors, Estrogen, chemistry; Software; Thermodynamics},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {0407404102},
  pmid = {15767587},
  timestamp = {2011.02.04},
  url = {http://dx.doi.org/10.1073/pnas.0407404102}
}

@ARTICLE{Oostenbrink2004a,
  author = {Chris Oostenbrink and Wilfred F van Gunsteren},
  title = {Free energies of binding of polychlorinated biphenyls to the estrogen
	receptor from a single simulation.},
  journal = {Proteins},
  year = {2004},
  volume = {54},
  pages = {237--246},
  number = {2},
  month = {Feb},
  abstract = {Relative free energies of binding to the ligand-binding domain of
	the estrogen receptor have been calculated for a series of 17 hydroxylated
	polychlorinated biphenyls. Because traditional thermodynamic integration
	or perturbation approaches are hardly feasible for these numbers
	of compounds, the one-step perturbation approach is applied and is
	shown to yield accurate results based on only two 2-ns molecular
	dynamics simulations of an unphysical, judiciously chosen, reference
	state. The mean absolute difference between the calculated and experimental
	binding free energies for the 17 compounds is 3.4 kJ/mol, which illustrates
	the accuracy of the GROMOS biomolecular force field used. Excluding
	the three largest ligands from the comparison reduces the deviation
	to 2.0 kJ/mol (i.e., < k(B)T). Apart from the relative free energy,
	structural information about the binding mode and binding orientation
	for every compound can also be extracted from the simulation, showing
	that a ligand bound to its receptor cannot be represented by a single
	conformation, but it samples an ensemble of different orientations.},
  doi = {10.1002/prot.10558},
  institution = {Laboratory of Physical Chemistry, Swiss Federal Institute of Technology
	Zürich, Zürich, Switzerland.},
  keywords = {Carbon; Computer Simulation; Ligands; Models, Molecular; Polychlorinated
	Biphenyls; Protein Binding; Protein Conformation; Receptors, Estrogen;
	Thermodynamics},
  owner = {emilio},
  pmid = {14696186},
  timestamp = {2010.06.02},
  url = {http://dx.doi.org/10.1002/prot.10558}
}

@ARTICLE{Orzco:Jorgensen:93,
  author = {Orozco, M. and Jorgensen, W. L. and Luque, F. J.},
  journal = {J. Comput. Chem.},
  year = {1993},
  volume = {14},
  pages = {1498},
  number = {12},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ozkan2002,
  author = {S. Banu Ozkan and Ken A Dill and Ivet Bahar},
  title = {Fast-folding protein kinetics, hidden intermediates, and the sequential
	stabilization model.},
  journal = {Protein Sci},
  year = {2002},
  volume = {11},
  pages = {1958--1970},
  number = {8},
  month = {Aug},
  abstract = {Do two-state proteins fold by pathways or funnels? Native-state hydrogen
	exchange experiments show discrete nonnative structures in equilibrium
	with the native state. These could be called hidden intermediates
	(HI) because their populations are small at equilibrium, and they
	are not detected in kinetic experiments. HIs have been invoked as
	disproof of funnel models, because funnel pictures appear to indicate
	(1) no specific sequences of events in folding; (2) a continuum,
	rather than a discrete ladder, of structures; and (3) smooth landscapes.
	In the present study, we solve the exact dynamics of a simple model.
	We find, instead, that the present microscopic model is indeed consistent
	with HIs and transition states, but such states occur in parallel,
	rather than along the single pathway predicted by the sequential
	stabilization model. At the microscopic level, we observe a huge
	multiplicity of trajectories. But at the macroscopic level, we observe
	two pathways of specific sequences of events that are relatively
	traditional except that they are in parallel, so there is not a single
	reaction coordinate. Using singular value decomposition, we show
	an accurate representation of the shapes of the model energy landscapes.
	They are highly complex funnels.},
  doi = {10.1110/ps.0207102},
  institution = {Center for Computational Biology and Bioinformatics, and Department
	of Molecular Genetics and Biochemistry, School of Medicine, University
	of Pittsburgh, Pennsylvania 15213, USA.},
  keywords = {Hydrogen-Ion Concentration; Kinetics; Mathematical Computing; Models,
	Chemical; Probability; Protein Conformation; Protein Folding; Proteins;
	Temperature; Thermodynamics; Time Factors},
  owner = {emilio},
  pmid = {12142450},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1110/ps.0207102}
}

@ARTICLE{Paliwal2011,
  author = {Paliwal, Himanshu and Shirts, Michael R.},
  title = {A Benchmark Test Set for Alchemical Free Energy Transformations and
	Its Use to Quantify Error in Common Free Energy Methods},
  journal = {J. Chem. Theory Comput.},
  year = {2011},
  pages = {Article ASAP},
  month = oct,
  abstract = {There is a significant need for improved tools to validate thermophysical
	quantities computed via molecular simulation. In this paper we present
	the initial version of a benchmark set of testing methods for calculating
	free energies of molecular transformation in solution. This set is
	based on molecular changes common to many molecular design problems,
	such as insertion and deletion of atomic sites and changing atomic
	partial charges. We use this benchmark set to compare the statistical
	efficiency, reliability, and quality of uncertainty estimates for
	a number of published free energy methods, including thermodynamic
	integration, free energy perturbation, the Bennett acceptance ratio
	(BAR) and its multistate equivalent MBAR. We identify MBAR as the
	consistently best performing method, though other methods are frequently
	comparable in reliability and accuracy in many cases. We demonstrate
	that assumptions of Gaussian distributed errors in free energies
	are usually valid for most methods studied. We demonstrate that bootstrap
	error estimation is a robust and useful technique for estimating
	statistical variance for all free energy methods studied. This benchmark
	set is provided in a number of different file formats with the hope
	of becoming a useful and general tool for method comparisons.

	There is a significant need for improved tools to validate thermophysical
	quantities computed via molecular simulation. In this paper we present
	the initial version of a benchmark set of testing methods for calculating
	free energies of molecular transformation in solution. This set is
	based on molecular changes common to many molecular design problems,
	such as insertion and deletion of atomic sites and changing atomic
	partial charges. We use this benchmark set to compare the statistical
	efficiency, reliability, and quality of uncertainty estimates for
	a number of published free energy methods, including thermodynamic
	integration, free energy perturbation, the Bennett acceptance ratio
	(BAR) and its multistate equivalent MBAR. We identify MBAR as the
	consistently best performing method, though other methods are frequently
	comparable in reliability and accuracy in many cases. We demonstrate
	that assumptions of Gaussian distributed errors in free energies
	are usually valid for most methods studied. We demonstrate that bootstrap
	error estimation is a robust and useful technique for estimating
	statistical variance for all free energy methods studied. This benchmark
	set is provided in a number of different file formats with the hope
	of becoming a useful and general tool for method comparisons.},
  booktitle = {Journal of Chemical Theory and Computation},
  comment = {doi: 10.1021/ct2003995},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.11.22},
  url = {http://dx.doi.org/10.1021/ct2003995}
}

@ARTICLE{Pangali:80,
  author = {Pangali, C. and Rao, M. and Berne, B. J.},
  journal = {Mol. Phys.},
  year = {1980},
  volume = {40},
  pages = {661-670},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pangali:Rao:Berne:79a,
  author = {Pangali, C. and Rao, M. and Berne, B. J.},
  title = {A Monte Carlo Simulation of the Hydrophobic Interaction},
  journal = {J. Chem. Phys.},
  year = {1979},
  volume = {71},
  pages = {2975-2981},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pangali:Rao:Berne:79b,
  author = {Pangali, C. and Rao, M. and Berne, B. J.},
  title = {Hydrophobic Hydration around a pair of Apolar Species in Water},
  journal = {J. Chem. Phys.},
  year = {1979},
  volume = {71},
  pages = {2975-2981},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Papazyan:Warshel:97,
  author = {Papazyan, A. and Warshel, A.},
  journal = {J. Chem. Phys.},
  year = {1997},
  volume = {107},
  pages = {7975},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Paris2009,
  author = {Kristina A Paris and Omar Haq and Anthony K Felts and Kalyan Das
	and Eddy Arnold and Ronald M Levy},
  title = {Conformational landscape of the human immunodeficiency virus type
	1 reverse transcriptase non-nucleoside inhibitor binding pocket:
	lessons for inhibitor design from a cluster analysis of many crystal
	structures.},
  journal = {J Med Chem},
  year = {2009},
  volume = {52},
  pages = {6413--6420},
  number = {20},
  month = {Oct},
  abstract = {Clustering of 99 available X-ray crystal structures of HIV-1 reverse
	transcriptase (RT) at the flexible non-nucleoside inhibitor binding
	pocket (NNIBP) provides information about features of the conformational
	landscape for binding non-nucleoside inhibitors (NNRTIs), including
	effects of mutation and crystal forms. The ensemble of NNIBP conformations
	is separated into eight discrete clusters based primarily on the
	position of the functionally important primer grip, the displacement
	of which is believed to be one of the mechanisms of inhibition of
	RT. Two of these clusters are populated by structures in which the
	primer grip exhibits novel conformations that differ from the predominant
	cluster by over 4 A and are induced by the unique inhibitors capravirine
	and rilpivirine/TMC278. This work identifies a new conformation of
	the NNIBP that may be used to design NNRTIs. It can also be used
	to guide more complete exploration of the NNIBP free energy landscape
	using advanced sampling techniques.},
  doi = {10.1021/jm900854h},
  institution = {Department of Chemistry and Chemical Biology, Rutgers University,
	610 Taylor Road, Piscataway, New Jersey 08854, USA.},
  keywords = {Binding Sites; Cluster Analysis; Crystallography, X-Ray; Drug Design;
	HIV Reverse Transcriptase; HIV-1; Humans; Ligands; Models, Molecular;
	Molecular Conformation; Nucleosides; Protein Conformation; Reverse
	Transcriptase Inhibitors},
  owner = {emilio},
  pmid = {19827836},
  timestamp = {2010.10.28},
  url = {http://dx.doi.org/10.1021/jm900854h}
}

@ARTICLE{Park:Levitt:96,
  author = {Park, B. and Levitt, M.},
  title = {Energy functions that discriminate {X}-ray and near-native folds
	from well-constructed decoys},
  journal = {J. Mol. Biol.},
  year = {1996},
  volume = {258},
  pages = {367-392},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Paschek:Hempel:Garcia:2008,
  author = {Paschek, D. and Hempel, S. and Garc\'{i}a, {A. E.}},
  title = {Computing the stability diagram of the Trp-cage miniprotein},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2008},
  volume = {105},
  pages = {17754-17759},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Paschek:Nymeyer:Garcia:2007,
  author = {Paschek, D. and Nymeyer, H. and Garc\'{i}a, {A. E.}},
  title = {Replica exchange simulation of reversible folding/unfolding of the
	Trp-cage miniprotein in explicit solvent: On the structure and possible
	role of internal water},
  journal = {J. Struct. Biol.},
  year = {2007},
  volume = {157},
  pages = {524-533},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Paschek2007,
  author = {Dietmar Paschek and Hugh Nymeyer and Angel E García},
  title = {Replica exchange simulation of reversible folding/unfolding of the
	Trp-cage miniprotein in explicit solvent: on the structure and possible
	role of internal water.},
  journal = {J Struct Biol},
  year = {2007},
  volume = {157},
  pages = {524--533},
  number = {3},
  month = {Mar},
  abstract = {We simulate the folding/unfolding equilibrium of the 20-residue miniprotein
	Trp-cage. We use replica exchange molecular dynamics simulations
	of the AMBER94 atomic detail model of the protein explicitly solvated
	by water, starting from a completely unfolded configuration. We employ
	a total of 40 replicas, covering the temperature range between 280
	and 538 K. Individual simulation lengths of 100 ns sum up to a total
	simulation time of about 4 micros. Without any bias, we observe the
	folding of the protein into the native state with an unfolding-transition
	temperature of about 440 K. The native state is characterized by
	a distribution of root mean square distances (RMSD) from the NMR
	data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration
	times of about 40 ns are required to yield convergence. A folded
	configuration in the entire extended ensemble is found to have a
	lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens
	up during thermal denaturation. In line with fluorescence quenching
	experiments, the Trp-residue sidechain gets hydrated when the protein
	opens up, roughly doubling the number of water molecules in the first
	solvation shell. We find the helical propensity of the helical domain
	of Trp-cage rather well preserved even at very high temperatures.
	In the folded state, we can identify states with one and two buried
	internal water molecules interconnecting parts of the Trp-cage molecule
	by hydrogen bonds. The loss of hydrogen bonds of these buried water
	molecules in the folded state with increasing temperature is likely
	to destabilize the folded state at elevated temperatures.},
  doi = {10.1016/j.jsb.2006.10.031},
  institution = {Physikalische Chemie, Otto-Hahn-Str. 6, Universität at Dortmund,
	D-44221 Dortmund, Germany. dietmar.paschek@udo.edu},
  keywords = {Computer Simulation; Protein Folding; Proteins; Solvents; Thermodynamics;
	Tryptophan; Water},
  owner = {emilio},
  pii = {S1047-8477(06)00329-7},
  pmid = {17293125},
  timestamp = {2010.10.27},
  url = {http://dx.doi.org/10.1016/j.jsb.2006.10.031}
}

@ARTICLE{Pascual:Silla:90,
  author = {Pascual-Ahuir, J. L. and Silla, E.},
  title = {GEPOL: An Improved Description of Molecular Surfaces. I. Building
	the Spherical Surface Set},
  journal = {J. Comp. Chem.},
  year = {1990},
  volume = {11},
  pages = {1047-1060},
  number = {9},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pashley:McGuiggan:Ninham:85,
  author = {Pashley, R. M. and McGuiggan, P. M. and Ninham, B. W.},
  title = {Attractive Forces Between Uncharged Hydrophobic Surfaces: Direct
	Measurements in Aqueous Solution},
  journal = {Science},
  year = {1985},
  volume = {229},
  pages = {1088},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Paulsen:Ornstein:1996,
  author = {Paulsen, {M. D.} and Ornstein, {R. L.}},
  title = {Binding free energy calculations for P450cam-substrate complexes},
  journal = {Protein Engineering},
  year = {1996},
  volume = {9},
  pages = {567--571},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pauwels1988,
  author = {R. Pauwels and J. Balzarini and M. Baba and R. Snoeck and D. Schols
	and P. Herdewijn and J. Desmyter and E. De Clercq},
  title = {Rapid and automated tetrazolium-based colorimetric assay for the
	detection of anti-HIV compounds.},
  journal = {J Virol Methods},
  year = {1988},
  volume = {20},
  pages = {309--321},
  number = {4},
  month = {Aug},
  abstract = {A rapid, sensitive and automated assay procedure was developed for
	the in vitro evaluation of anti-HIV agents. An HTLV-I transformed
	T4-cell line, MT-4, which was previously shown by Koyanagi et al.
	(1985) to be highly susceptible to, and permissive for, HIV infection,
	served as the target cell line. Inhibition of the HIV-induced cytopathic
	effect was used as the end point. The viability of both HIV- and
	mock-infected cells was assessed spectrophotometrically via the in
	situ reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium
	bromide (MTT). The procedure was optimized as to make optimal use
	of multichannel pipettes, microprocessor-controlled dispensing and
	optical density reading. The absorbance ratio of the mock-infected
	control to the HIV-infected samples was about 20. This allowed an
	accurate determination of the 50\% effective doses, as demonstrated
	for 3'-azido-2',3'-dideoxythymidine (AZT), 2',3'-dideoxycytidine
	(ddCyd), dextran sulfate and heparin. The technique significantly
	reduced labor time as compared to the trypan blue exclusion method,
	and permits the evaluation of large numbers of compounds for their
	anti-HIV activity.},
  institution = {Department of Human Biology, Rega Institute for Medical Research,
	Katholieke Universiteit Leuven, Belgium.},
  keywords = {Acquired Immunodeficiency Syndrome, drug therapy; Antiviral Agents;
	Cell Line, Transformed; Colorimetry, methods; Cytopathogenic Effect,
	Viral, drug effects; Dextran Sulfate; Dextrans, pharmacology; Dideoxynucleosides,
	pharmacology; Drug Evaluation, Preclinical, methods; HIV, drug effects;
	Heparin, pharmacology; Humans; Tetrazolium Salts; Thiazoles; Zalcitabine;
	Zidovudine, pharmacology},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {2460479},
  timestamp = {2012.02.23}
}

@ARTICLE{Payne:Matubayasi:Reed:Levy:97,
  author = {Payne, V. A. and Matubayasi, N. and Reed Murphy, L. and Levy, R.
	M.},
  title = {Monte Carlo Study of the Effect of Pressure on Hydrophobic Association},
  journal = {J. Phys. Chem. B},
  year = {1997},
  volume = {101},
  pages = {2054-2060},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pearlman:Kollman:89,
  author = {Pearlman, D. A. and Kollman, P. A.},
  title = {A New Method for Carrying Out Free Energy Perturbation Calculations:
	Dynamically Modified Windows},
  journal = {J. Chem. Phys.},
  year = {1989},
  volume = {90},
  pages = {2460},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pellegrini:Field:2002,
  author = {E. Pellegrini and M. J. Field},
  title = {A generalized-Born solvation model for macromolecular hybrid-potential
	calculations},
  journal = {J. Phys. Chem. A},
  year = {2002},
  volume = {106},
  pages = {1316-1326},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Perola2004a,
  author = {Emanuele Perola and Paul S Charifson},
  title = {Conformational analysis of drug-like molecules bound to proteins:
	an extensive study of ligand reorganization upon binding.},
  journal = {J Med Chem},
  year = {2004},
  volume = {47},
  pages = {2499--2510},
  number = {10},
  month = {May},
  abstract = {This paper describes a large-scale study on the nature and the energetics
	of the conformational changes drug-like molecules experience upon
	binding. Ligand strain energies and conformational reorganization
	were analyzed with different computational methods on 150 crystal
	structures of pharmaceutically relevant protein-ligand complexes.
	The common knowledge that ligands rarely bind in their lowest calculated
	energy conformation was confirmed. Additionally, we found that over
	60\% of the ligands do not bind in a local minimum conformation.
	While approximately 60\% of the ligands were calculated to bind with
	strain energies lower than 5 kcal/mol, strain energies over 9 kcal/mol
	were calculated in at least 10\% of the cases regardless of the method
	used. A clear correlation was found between acceptable strain energy
	and ligand flexibility, while there was no correlation between strain
	energy and binding affinity, thus indicating that expensive conformational
	rearrangements can be tolerated in some cases without overly penalizing
	the tightness of binding. On the basis of the trends observed, thresholds
	for the acceptable strain energies of bioactive conformations were
	defined with consideration of the impact of ligand flexibility. An
	analysis of the degree of folding of the bound ligands confirmed
	the general tendency of small molecules to bind in an extended conformation.
	The results suggest that the unfolding of hydrophobic ligands during
	binding, which exposes hydrophobic surfaces to contact with protein
	residues, could be one of the factors accounting for high reorganization
	energies. Finally, different methods for conformational analysis
	were evaluated, and guidelines were defined to maximize the prevalence
	of bioactive conformations in computationally generated ensembles.},
  comment = {Ligand reorganization},
  doi = {10.1021/jm030563w},
  institution = {Vertex Pharmaceuticals, 130 Waverly Street, Cambridge, Massachusetts
	02139, USA. emanuele_perola@vrtx.com},
  keywords = {Drug Design; Endopeptidases; Ligands; Molecular Conformation; Pharmaceutical
	Preparations; Phosphotransferases; Protein Binding; Protein Folding;
	Proteins; Thermodynamics},
  owner = {emilio},
  pmid = {15115393},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1021/jm030563w}
}

@ARTICLE{Peterson:95,
  author = {Peterson, B. R. and Walliman, P. and Carcanague, D. R. and Diederich,
	F.},
  title = {Steroid complexation by cyclophane receptors in aqueous solution:
	substrate selectivity, enthalpic driving force for cavity inclusion,
	and enthalpy-entropy compensation},
  journal = {Tetrahedron},
  year = {1995},
  volume = {51},
  pages = {401-421},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Petitjean:94,
  author = {Petitjean, M.},
  title = {On the Analytical Calculation of van der Waals Surfaces and Volumes:
	Some Numerical Aspects},
  journal = {J. Comp. Chem.},
  year = {1994},
  volume = {15},
  pages = {507-523},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Petrey:Honig:2000,
  author = {Petrey, D. and Honig, B.},
  title = {Free energy determinants of tertiary structure and the evaluation
	of protein models},
  journal = {Protein Science},
  year = {2000},
  volume = {9},
  pages = {2181-2191},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@INPROCEEDINGS{Petrini:2003,
  author = {Petrini, F. and Kerbyson, {D. J.} and Pakin, S.},
  title = {The Case of the Missing Supercomputer Performance: Achieving Optimal
	Performance on the 8,192 Processors of {ASCI Q}},
  booktitle = {SC '03: Proceedings of the 2003 ACM/IEEE conference on Supercomputing},
  year = {2003},
  pages = {55},
  address = {Washington, DC, USA},
  publisher = {IEEE Computer Society},
  isbn = {1-58113-695-1},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Piana2007,
  author = {Piana, Stefano and Laio, Alessandro},
  title = {A Bias-Exchange Approach to Protein Folding},
  journal = {The Journal of Physical Chemistry B},
  year = {2007},
  volume = {111},
  pages = {4553--4559},
  number = {17},
  month = may,
  abstract = {By suitably extending a recent approach [Bussi, G.; et al. J. Am.
	Chem. Soc. 2006, 128, 13435] we introduce a powerful methodology
	that allows the parallel reconstruction of the free energy of a system
	in a virtually unlimited number of variables. Multiple metadynamics
	simulations of the same system at the same temperature are performed,
	biasing each replica with a time-dependent potential constructed
	in a different set of collective variables. Exchanges between the
	bias potentials in the different variables are periodically allowed
	according to a replica exchange scheme. Due to the efficaciously
	multidimensional nature of the bias the method allows exploring complex
	free energy landscapes with high efficiency. The usefulness of the
	method is demonstrated by performing an atomistic simulation in explicit
	solvent of the folding of a Triptophane cage miniprotein. It is shown
	that the folding free energy landscape can be fully characterized
	starting from an extended conformation with use of only 40 ns of
	simulation on 8 replicas.},
  comment = {doi: 10.1021/jp067873l},
  issn = {1520-6106},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.01.13},
  url = {http://dx.doi.org/10.1021/jp067873l}
}

@ARTICLE{Pierotti:76,
  author = {Pierotti, R. A.},
  title = {A Scaled Particle Theory of Aqueous and Nonaqueous Solutions},
  journal = {Chemical Reviews},
  year = {1976},
  volume = {76},
  pages = {717-26},
  number = {6},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pitarch:Moliner:Ahuir:Silla:Tunon:96,
  author = {Pitarch, J. and Moliner, V. and Pascual-Ahuir, J.-L. and Silla, A.
	and Tu\~{n}\'{o}n, I.},
  title = {Can Hydrophobic Interactions Be Correctly Reproduced by the Continuum
	Models?},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {9955-9959},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pitera:vanGunsteren:2001,
  author = {Pitera, J. W. and van Gunsteren, W. F.},
  title = {The Importance of Solute-Solvent van der Waals Interactions with
	Interior Atoms of Biopolymers},
  journal = {J. Am. Chem. Soc.},
  year = {2001},
  volume = {123},
  pages = {3163-3164},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pitera:Swope:2003,
  author = {Pitera, {J. W.} and Swope, W. },
  title = {Understanding folding and design: Replica exchange simulations of
	of Trp-cage miniproteins},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2003},
  volume = {100},
  pages = {7587-7592},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pohorille2010,
  author = {Andrew Pohorille and Christopher Jarzynski and Christophe Chipot},
  title = {Good practices in free-energy calculations.},
  journal = {J. Phys. Chem. B},
  year = {2010},
  volume = {114},
  pages = {10235--10253},
  number = {32},
  month = {Aug},
  abstract = {As access to computational resources continues to increase, free-energy
	calculations have emerged as a powerful tool that can play a predictive
	role in a wide range of research areas. Yet, the reliability of these
	calculations can often be improved significantly if a number of precepts,
	or good practices, are followed. Although the theory upon which these
	good practices rely has largely been known for many years, it is
	often overlooked or simply ignored. In other cases, the theoretical
	developments are too recent for their potential to be fully grasped
	and merged into popular platforms for the computation of free-energy
	differences. In this contribution, the current best practices for
	carrying out free-energy calculations using free energy perturbation
	and nonequilibrium work methods are discussed, demonstrating that
	at little to no additional cost, free-energy estimates could be markedly
	improved and bounded by meaningful error estimates. Monitoring the
	probability distributions that underlie the transformation between
	the states of interest, performing the calculation bidirectionally,
	stratifying the reaction pathway, and choosing the most appropriate
	paradigms and algorithms for transforming between states offer significant
	gains in both accuracy and precision.},
  doi = {10.1021/jp102971x},
  institution = {NASA Ames Research Center, Exobiology Branch, Mail Stop 239-4, Moffett
	Field, California, 94035-1000, USA.},
  keywords = {Algorithms; Computer Simulation; Entropy; Mathematics; Models, Molecular;
	Models, Theoretical; Thermodynamics},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {20701361},
  timestamp = {2011.07.15},
  url = {http://dx.doi.org/10.1021/jp102971x}
}

@ARTICLE{Pohorille1990a,
  author = {A. Pohorille and L. R. Pratt},
  title = {Cavities in molecular liquids and the theory of hydrophobic solubilities.},
  journal = {J. Am. Chem. Soc.},
  year = {1990},
  volume = {112},
  pages = {5066--5074},
  number = {13},
  abstract = {Thermal configurational data on neat liquids are used to obtain the
	work of formation of hard spherical cavities of atomic size in six
	molecular solvents: n-hexane, n-dodecane, n-undecyl alcohol, chloroform,
	carbon tetrachloride, and water. These results are used to test a
	recent suggestion that the differences between nonaqueous solvents
	and liquid water in solvation of inert gases are not principally
	due to the hydrogen-bonded structure of liquid water but rather to
	the comparatively small size of the water molecule. The frequencies
	of occurrence of cavities in liquid water can be meaningfully distinguished
	from those in the organic solvents. Liquid water has a larger fractional
	free volume, but that free volume is distributed in smaller packets.
	With respect to cavity work, water is compared to a solvent of the
	same molecular density and composed of hard spheres of the same size
	as the water molecule. That comparison indicates that the hard-sphere
	liquid finds more ways to configure its free volume in order to accommodate
	an atomic solute of substantial size and thus, would be more favorable
	solvent for inert gases. The scaled particle model of inert gas solubility
	in liquid water predicts cavity works 20\% below the numerical data
	for TIP4P water at 300 K and 1.0 g/cm3 for cavity radii near 2.0
	angstroms. It is argued that the sign of this difference is just
	the sign that ought to be expected and that the magnitude of this
	difference measures structural differences between water and the
	directly comparable hard-sphere liquid. In conjunction with previous
	data, these results indicate that atomic sized cavities should be
	considered submacroscopic.},
  institution = {ARC},
  keywords = {Alkanes; Carbon Tetrachloride; Chloroform; Hexanes; Mathematics; Models,
	Chemical; Molecular Structure; Solubility; Solvents; Temperature;
	Water},
  owner = {emilio},
  pmid = {11540917},
  timestamp = {2010.05.20}
}

@ARTICLE{Postma:Berendsen:Haak:82,
  author = {Postma, J. P. M. and Berendsen, H. J. C. and Haak, J. R.},
  journal = {Faraday Symp. Chem. Soc.},
  year = {1982},
  volume = {17},
  pages = {55},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Prabhu:Sharp:2006,
  author = {Prabhu, N. and Sharp, M.},
  title = {Protein--Solvent Interactions},
  journal = {Chem. Rev.},
  year = {2006},
  volume = {106},
  pages = {1616-1623},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Prada-Gracia2009,
  author = {Prada-Gracia, Diego and Gómez-Gardeñes, Jesús and Echenique, Pablo
	and Falo, Fernando},
  title = {Exploring the Free Energy Landscape: From Dynamics to Networks and
	Back},
  journal = {PLoS Comput Biol},
  year = {2009},
  volume = {5},
  pages = {e1000415--},
  number = {6},
  month = jun,
  abstract = {<title>Author Summary</title> <p>A complete description of complex
	polymers, such as proteins, includes information about their structure
	and their dynamics. In particular it is of utmost importance to answer
	the following questions: What are the structural conformations possible?
	Is there any relevant hierarchy among these conformers? What are
	the transition paths between them? These and other questions can
	be addressed by analyzing in an efficient way the Free Energy Landscape
	of the system. With this knowledge, several problems about biomolecular
	reactions (such as enzymatic activity, protein folding, protein deposition
	diseases, etc.) can be tackled. In this article we show how to efficiently
	describe the Free Energy Landscape for small and large peptides.
	By mapping the trajectories of molecular dynamics simulations into
	a graph (the Conformational Markov Network) and unveiling its structural
	organization, we obtain a coarse grained description of the protein
	dynamics across the Free Energy Landscape in terms of the relevant
	kinetic magnitudes of the system. Therefore, we show the way to bridge
	the gap between the microscopic dynamics and the macroscopic kinetics
	by means of a mesoscopic description of the associated Conformational
	Markov Network. Along this path the compromise between the physical
	nature of the process and the magnitudes that characterize the network
	is carefully kept to assure the reliability of the results shown.</p>},
  owner = {emilio},
  publisher = {Public Library of Science},
  timestamp = {2011.01.13},
  url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1000415}
}

@INBOOK{Pratt:BookChapter:FreeEnergy:2007,
  chapter = {Potential Distribution Methods and Free Energy Models of Molecular
	Solutions},
  pages = {323-352},
  title = {Free Energy Calculations, Theory and Applications in Chemistry and
	Biology},
  publisher = {Springer},
  year = {2007},
  editor = {Christophe Chipot and Andrew Pohorille},
  author = {L.R. Pratt and D. Asthagiri},
  owner = {emilio},
  timestamp = {2010.04.30}
}

@ARTICLE{Pratt:Chandler:80,
  author = {Pratt, L. R. and Chandler, D.},
  title = {Effects of Solute-Solvent Attractive Forces on Hydrophobic Correlations},
  journal = {J. Chem. Phys.},
  year = {1980},
  volume = {73},
  pages = {3434-41},
  number = {7},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pratt:Chandler:77,
  author = {Pratt, L. R. and Chandler, D.},
  title = {Theory of the Hydrophobic Effect},
  journal = {J. Chem. Phys.},
  year = {1977},
  volume = {67},
  pages = {3683-3704},
  number = {8},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pratt:94,
  author = {Pratt, L. R. and Hummer, G. and Garcia, A.},
  journal = {Biophys. Chem.},
  year = {1994},
  volume = {51},
  pages = {147-160},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Pratt1992,
  author = {L. R. Pratt and A. Pohorille},
  title = {Theory of hydrophobicity: transient cavities in molecular liquids.},
  journal = {Proc Natl Acad Sci U S A},
  year = {1992},
  volume = {89},
  pages = {2995--2999},
  month = {Apr},
  abstract = {Observation of the size distribution of transient cavities in computer
	simulations of water, n-hexane, and n-dodecane under benchtop conditions
	shows that the sizes of cavities are more sharply defined in liquid
	water but the most-probable-size cavities are about the same size
	in each of these liquids. The calculated solvent atomic density in
	contact with these cavities shows that water applies more force per
	unit area of cavity surface than do the hydrocarbon liquids. This
	contact density, or "squeezing" force, reaches a maximum near cavity
	diameters of 2.4 angstroms. The results for liquid water are compared
	to the predictions of simple theories and, in addition, to results
	for a reference simple liquid. The numerical data for water at a
	range of temperatures are analyzed to extract a surface free energy
	contribution to the work of formation of atomic-size cavities. Comparison
	with the liquid-vapor interfacial tensions of the model liquids studied
	here indicates that the surface free energies extracted for atomic-size
	cavities cannot be accurately identified with the macroscopic surface
	tensions of the systems.},
  institution = {ARC},
  keywords = {Alkanes; Computer Simulation; Hexanes; Hydrocarbons; Mathematics;
	Models, Chemical; Models, Theoretical; Solubility; Solvents; Water},
  owner = {emilio},
  pmid = {11537863},
  timestamp = {2010.04.30}
}

@ARTICLE{Privalov:Gill:88,
  author = {Privalov, P. L. and Gill, S. J.},
  journal = {Adv. Protein Chem.},
  year = {1988},
  volume = {39},
  pages = {191},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Privalov:Makhatadze:93,
  author = {Privalov, P. L. and Makhatadze, G. I.},
  title = {Contribution of Hydration to Protein Folding Thermodynamics. I. The
	Entropy and {G}ibbs Energy of Hydration},
  journal = {J. Mol. Biol.},
  year = {1993},
  volume = {232},
  pages = {660-679},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Privalov:Makhatadze:92,
  author = {Privalov, P. L. and Makhatadze, G. I.},
  title = {Contribution of Hydration and Non-covalent Interactions to the Heat
	Capacity Effect on Protein Unfolding},
  journal = {J. Mol. Biol.},
  year = {1992},
  volume = {224},
  pages = {715-723},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Purisima2010,
  author = {Enrico O Purisima and Christopher R Corbeil and Traian Sulea},
  title = {Rapid prediction of solvation free energy. 3. Application to the
	SAMPL2 challenge.},
  journal = {J Comput Aided Mol Des},
  year = {2010},
  month = {Apr},
  abstract = {The SAMPL2 hydration free energy blind prediction challenge consisted
	of a data set of 41 molecules divided into three subsets: explanatory,
	obscure and investigatory, where experimental hydration free energies
	were given for the explanatory, withheld for the obscure, and not
	known for the investigatory molecules. We employed two solvation
	models for this challenge, a linear interaction energy (LIE) model
	based on explicit-water molecular dynamics simulations, and the first-shell
	hydration (FiSH) continuum model previously calibrated to mimic LIE
	data. On the 23 compounds from the obscure (blind) dataset, the prospectively
	submitted LIE and FiSH models provided predictions highly correlated
	with experimental hydration free energy data, with mean-unsigned-errors
	of 1.69 and 1.71 kcal/mol, respectively. We investigated several
	parameters that may affect the performance of these models, namely,
	the solute flexibility for the LIE explicit-solvent model, the solute
	partial charging method, and the incorporation of the difference
	in intramolecular energy between gas and solution phases for both
	models. We extended this analysis to the various chemical classes
	that can be formed within the SAMPL2 dataset. Our results strengthen
	previous findings on the excellent accuracy and transferability of
	the LIE explicit-solvent approach to predict transfer free energies
	across a wide spectrum of functional classes. Further, the current
	results on the SAMPL2 test dataset provide additional support for
	the FiSH continuum model as a fast yet accurate alternative to the
	LIE explicit-solvent model. Overall, both the LIE explicit-solvent
	model and the FiSH continuum solvation model show considerable improvement
	on the SAMPL2 data set over our previous continuum electrostatics-dispersion
	solvation model used in the SAMPL1 blind challenge.},
  doi = {10.1007/s10822-010-9341-9},
  institution = {Biotechnology Research Institute, National Research Council Canada,
	6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada, enrico.purisima@cnrc-nrc.gc.ca.},
  owner = {emilio},
  pmid = {20414699},
  timestamp = {2010.05.20},
  url = {http://dx.doi.org/10.1007/s10822-010-9341-9}
}

@ARTICLE{Purisima2009,
  author = {Enrico O Purisima and Traian Sulea},
  title = {Restoring charge asymmetry in continuum electrostatics calculations
	of hydration free energies.},
  journal = {J Phys Chem B},
  year = {2009},
  volume = {113},
  pages = {8206--8209},
  number = {24},
  month = {Jun},
  abstract = {Implicit solvation models are symmetric with respect to charge inversion.
	On the other hand, explicit solvent simulations show significant
	asymmetry in hydration free energies with respect to charge reversal.
	It has not been obvious how implicit solvation models can be modified
	in a general way to address this serious shortcoming. We solve this
	problem by using the induced surface charge density (ISCD) obtained
	from a boundary element solution of the Poisson equation to derive
	a simple customized correction for the Born radius of each atom.
	This simple correction restores the charge asymmetry and reproduces
	the hydration free energies from free energy perturbation calculations
	with a high degree of fidelity. The induced surface charge density
	profile of an atom essentially provides a measure of the average
	preferred orientation of a water molecule in the first solvation
	shell, thereby allowing a proper assignment of the dielectric boundary.
	We refer to these modified radii as ISCD-corrected Born radii.},
  doi = {10.1021/jp9020799},
  institution = {Biotechnology Research Institute, National Research Council of Canada,
	6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2. Enrico.Purisima@nrc.ca},
  keywords = {Computer Simulation; Models, Chemical; Static Electricity; Surface
	Properties; Thermodynamics},
  owner = {emilio},
  pmid = {19459599},
  timestamp = {2010.05.20},
  url = {http://dx.doi.org/10.1021/jp9020799}
}

@ARTICLE{Qian:Chan:96,
  author = {Qian, H. and Chan, S. I.},
  title = {Interactions Between a Helical Residue and Tertiary Structures: Helix
	Propensities in Small Peptides and in Native Proteins},
  journal = {J. Mol. Biol.},
  year = {1996},
  volume = {261},
  pages = {279-288},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Qian:Hopfield:97,
  author = {Qian, H. and Hopfield, J. J.},
  title = { Entropy-enthalpy compensation: Perturbation and relaxation in thermodynamic
	systems},
  journal = {J. Chem. Phys.},
  year = {1996},
  volume = {105},
  pages = {9292},
  number = {20},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Qiu:Shenkin:Hollinger:Still:97,
  author = {Qiu, D. and Shenkin, P. S. and Hollinger, F. P. and Still, C. W.},
  title = {The GB/SA continuum model for solvation. A fast analystical method
	for the calculation of approximate Born radii},
  journal = {J. Phys. Chem. A},
  year = {1997},
  volume = {101},
  pages = {3005-3014},
  owner = {emilio},
  timestamp = {2010.11.01}
}

@ARTICLE{Radmer:Kollman:96,
  author = {Radmer, R. J. and Kollman, P. A.},
  title = {Free Energy Calculation Methods: A theoretical and empirical comparison
	of numerical errors and a new method for qualitative estimates of
	free energy changes},
  journal = {J. Comput. Chem.},
  year = {1997},
  volume = {18},
  pages = {902-19},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Rankin2003,
  author = {Kathryn N Rankin and Traian Sulea and Enrico O Purisima},
  title = {On the transferability of hydration-parametrized continuum electrostatics
	models to solvated binding calculations.},
  journal = {J Comput Chem},
  year = {2003},
  volume = {24},
  pages = {954--962},
  number = {8},
  month = {Jun},
  abstract = {Using molecular mechanics force field partial atomic charges, we show
	the nonuniqueness of the parametrization of continuum electrostatics
	models with respect to solute atomic radii and interior dielectric
	constant based on hydration (vacuum-to-water transfer) free energy
	data available for small molecules. Moreover, parameter sets that
	are optimal and equivalent for hydration free energy calculations
	lead to large variations of calculated absolute and relative electrostatic
	binding free energies. Hence, parametrization of solvation effects
	based on hydration data, although a necessary condition, is not sufficient
	to guarantee its transferability to the calculation of binding free
	energies in solution.},
  doi = {10.1002/jcc.10261},
  institution = {Biotechnology Research Institute, National Research Council of Canada,
	6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada.},
  owner = {emilio},
  pmid = {12720316},
  timestamp = {2010.05.20},
  url = {http://dx.doi.org/10.1002/jcc.10261}
}

@ARTICLE{Rao:Singh:89,
  author = {Rao, B. and Singh, U.},
  journal = {J. Am. Chem. Soc.},
  year = {1989},
  volume = {111},
  pages = {3125},
  number = {9},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Rapp:Friesner:99,
  author = {C. S. Rapp and R. A. Friesner},
  title = {Prediction of loop geometries using a generalized Born model of solvation
	Effects},
  journal = {Proteins: Struct., Funct., Genet.},
  year = {1999},
  volume = {35},
  pages = {173-183},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ravindranathan:Gallicchio:Levy:2006,
  author = {Ravindranathan, K.P. and Gallicchio, E. and Friesner, R. A. and McDermott,
	A. E. and Levy, R. M.},
  title = {Conformational equilibrium of cytochrome P450 BM-3 complexed with
	N-Palmitoylglycine: A replica exchange molecular dynamics study},
  journal = {J. Am. Chem. Soc.},
  year = {2006},
  volume = {128},
  pages = {5786--5791},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ravindranathan2005,
  author = {Ravindranathan, Krishna Pratap and Gallicchio, Emilio and Levy, Ronald
	M.},
  title = {Conformational Equilibria and Free Energy Profiles for the Allosteric
	Transition of the Ribose-binding Protein},
  journal = {Journal of Molecular Biology},
  year = {2005},
  volume = {353},
  pages = {196--210},
  number = {1},
  month = oct,
  abstract = {The ribose-binding protein (RBP) is a sugar-binding bacterial periplasmic
	protein whose function is associated with a large allosteric conformational
	change from an open to a closed conformation upon binding to ribose.
	The crystal structures of RBP in open and closed conformations have
	been solved. It has been hypothesized that the open and closed conformations
	exist in a dynamic equilibrium in solution, and that sugar binding
	shifts the population from open conformations to closed conformations.
	Here, we study by computer simulations the thermodynamic changes
	that accompany this conformational change, and model the structural
	changes that accompany the allosteric transition, using umbrella
	sampling molecular dynamics and the weighted histogram analysis method.
	The open state is comprised of a diverse ensemble of conformations;
	the open ribose-free X-ray crystal conformations being representative
	of this ensemble. The unligated open form of RBP is stabilized by
	conformational entropy. The simulations predict detectable populations
	of closed ribose-free conformations in solution. Additional interdomain
	hydrogen bonds stabilize this state. The predicted shift in equilibrium
	from the open to the closed state on binding to ribose is in agreement
	with experiments. This is driven by the energetic stabilization of
	the closed conformation due to ribose-protein interactions. We also
	observe a significant population of a hitherto unobserved ribose-bound
	partially open state. We believe that this state is the one that
	has been suggested to play a role in the transfer of ribose to the
	membrane-bound permease complex.},
  issn = {0022-2836},
  keywords = {ribose-binding protein, ligand-induced conformational change, protein
	allostery, umbrella sampling molecular dynamics, free energy profiles},
  owner = {emilio},
  timestamp = {2011.01.13},
  url = {http://www.sciencedirect.com/science/article/B6WK7-4GY844J-3/2/0884cfa27a6f6a823ad5932ffe934f32}
}

@ARTICLE{Ravindranathan:Gallicchio:Levy:2005,
  author = {Ravindranathan, {K. P.} and Gallicchio, E. and Levy, {R. M.}},
  title = {Conformational Equilibria and Free Energy Profiles for the Allosteric
	Transition of the Ribose Binding Protein},
  journal = {J. Mol. Biol.},
  year = {2005},
  volume = {353},
  pages = {196--210},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ravindranathan:Gallicchio:2007,
  author = {Ravindranathan, {K. P.} and Gallicchio, E. and McDermott, {A. E.}
	and Levy, {R. M.}},
  title = {Conformational dynamics of substrate in the active site of cytochrome
	{P450 BM-3/NPG} complex: Insights from {NMR} order parameters},
  journal = {J. Am. Chem. Soc.},
  year = {2007},
  volume = {129},
  pages = {474--475},
  owner = {emilio},
  timestamp = {2010.10.28}
}

@ARTICLE{Rekharsky1998,
  author = {Mikhail V. Rekharsky and Yoshihisa Inoue},
  title = {Complexation Thermodynamics of Cyclodextrins.},
  journal = {Chem Rev},
  year = {1998},
  volume = {98},
  pages = {1875--1918},
  number = {5},
  month = {Jul},
  institution = {Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka
	565-0085, Japan, and Department of Molecular Chemistry, Faculty of
	Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {cr970015o},
  pmid = {11848952},
  timestamp = {2011.06.29}
}

@ARTICLE{Rekharsky2007,
  author = {Mikhail V Rekharsky and Tadashi Mori and Cheng Yang and Young Ho
	Ko and N. Selvapalam and Hyunuk Kim and David Sobransingh and Angel
	E Kaifer and Simin Liu and Lyle Isaacs and Wei Chen and Sarvin Moghaddam
	and Michael K Gilson and Kimoon Kim and Yoshihisa Inoue},
  title = {A synthetic host-guest system achieves avidin-biotin affinity by
	overcoming enthalpy-entropy compensation.},
  journal = {Proc Natl Acad Sci U S A},
  year = {2007},
  volume = {104},
  pages = {20737--20742},
  number = {52},
  month = {Dec},
  abstract = {The molecular host cucurbit[7]uril forms an extremely stable inclusion
	complex with the dicationic ferrocene derivative bis(trimethylammoniomethyl)ferrocene
	in aqueous solution. The equilibrium association constant for this
	host-guest pair is 3 x 10(15) M(-1) (K(d) = 3 x 10(-16) M), equivalent
	to that exhibited by the avidin-biotin pair. Although purely synthetic
	systems with larger association constants have been reported, the
	present one is unique because it does not rely on polyvalency. Instead,
	it achieves its extreme affinity by overcoming the compensatory enthalpy-entropy
	relationship usually observed in supramolecular complexes. Its disproportionately
	low entropic cost is traced to extensive host desolvation and to
	the rigidity of both the host and the guest.},
  doi = {10.1073/pnas.0706407105},
  institution = {ICORP Entropy Control Project (JST) and Department of Applied Chemistry,
	Osaka University, Yamada-oka, Suita 565-0871, Japan.},
  keywords = {Avidin; Biotin; Biotinylation; Bridged Compounds; Calorimetry; Chemistry;
	Crystallography, X-Ray; Entropy; Hydrogen Bonding; Imidazoles; Kinetics;
	Models, Molecular; Molecular Conformation; Molecular Structure; Streptavidin;
	Thermodynamics},
  owner = {emilio},
  pii = {0706407105},
  pmid = {18093926},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1073/pnas.0706407105}
}

@ARTICLE{Resat:McCammon:96,
  author = {Resat, H. and McCammon, J. A.},
  journal = {J. Chem. Phys.},
  year = {1996},
  volume = {104},
  pages = {7645-7651},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Reynolds:Gilbert:Tanford:74,
  author = {J. A. Reynolds and D. B. Gilbert and C. Tanford},
  journal = {Proc. Natl. Acad. Sci. U.S.A.},
  year = {1974},
  volume = {71},
  pages = {2925},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Rhee:Pande:2003,
  author = {Rhee, {Y. M.} and Pande, {V. S.} },
  title = {Multiplexed-Replica Exchange Molecular Dynamics Method for Protein
	Folding Simulation},
  journal = {Biophysical Journal},
  year = {2003},
  volume = {84},
  pages = {775--786},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Rick2006,
  author = {Rick, Steven W.},
  title = {Increasing the Efficiency of Free Energy Calculations Using Parallel
	Tempering and Histogram Reweighting},
  journal = {J. Chem. Theory Comput.},
  year = {2006},
  volume = {2},
  pages = {939--946},
  number = {4},
  month = jul,
  abstract = {Free energy calculations from molecular simulations using thermodynamic
	integration or free energy perturbation require long simulation times
	to achieve sufficient precision. If entropic and enthalpic components
	of the free energy are desired, then the computational requirements
	are larger still. Here we present how parallel tempering (PT) Monte
	Carlo and weighted histogram analysis method (WHAM) can be used to
	improve the efficiency of free energy calculations. For both methods,
	which can be used separately or together, simulations at more than
	one temperature are performed. The same additional temperatures are
	often used to determine entropy changes. The results, for the aqueous
	solvation of n-butane and methane, show noticeable improvement in
	the precision of the free energy and entropy changes. The PT and
	WHAM methods can give similar error bars as conventional molecular
	dynamics in half the simulation time. The methods offer an efficient
	procedure for calculating free energy, entropy, and enthalpy changes
	in which free energy calculations are performed in parallel for a
	small number of closely spaced temperatures (for example, as here,
	at three temperatures:  298 K and 298 ± 15 K), and WHAM is used to
	enhance the data at each temperature.},
  comment = {doi: 10.1021/ct050207o},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1021/ct050207o}
}

@ARTICLE{Rick:Berne:97,
  author = {Rick, S. W. and Berne, B. J.},
  title = {The Free Energy of the Hydrophobic Interaction from Molecular Dynamics
	Simulations: the Effects of Solute and Solvent Polarizability},
  journal = {J Phys. Chem. B},
  year = {1997},
  volume = {101},
  pages = {10488},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Rizzo:Tirado:Jorgensen:2001,
  author = {Rizzo, R.C. and Tirado-{R}ives, J. and Jorgensen, W. L.},
  title = {Estimation of binding affinities for {HEPT} and nevirapine analogues
	with {HIV}-1 reverse transcriptase via {M}onte {C}arlo simulations},
  journal = {J. Med. Chem.},
  year = {2001},
  volume = {44},
  pages = {145--154},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Rizzo:Jorgensen:99,
  author = {Rizzo, R. C. and Jorgensen, W. L.},
  title = {OPLS All-Atom Model for Amines: Resolution of the Amine Hydration
	Problem},
  journal = {J. Am. Chem. Soc.},
  year = {1999},
  volume = {121},
  pages = {4827-4836},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Rizzo:Blagovic:Jorgensen:2002,
  author = {Rizzo, {R. C.} and Udier-Blagovi\'{c}, M. and Wang, {D.-P.} and Watkins,
	{E. K.} and Kroeger Smith, {M. B.} and Smith Jr., {R. H.} and Tirado-Rives,
	J. and Jorgensen, {W. L.}},
  title = {Prediction of activity of nonnucleoside inhibitors with {HIV-1} reverse
	transcriptase based on {M}onte {C}arlo simulations},
  journal = {J. Med. Chem.},
  year = {2002},
  volume = {45},
  pages = {2970--2987},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Robbins2010,
  author = {Arthur H Robbins and Roxana M Coman and Edith Bracho-Sanchez and
	Marty A Fernandez and C. Taylor Gilliland and Mi Li and Mavis Agbandje-McKenna
	and Alexander Wlodawer and Ben M Dunn and Robert McKenna},
  title = {Structure of the unbound form of HIV-1 subtype A protease: comparison
	with unbound forms of proteases from other HIV subtypes.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {2010},
  volume = {66},
  pages = {233--242},
  number = {Pt 3},
  month = {Mar},
  abstract = {The crystal structure of the unbound form of HIV-1 subtype A protease
	(PR) has been determined to 1.7 A resolution and refined as a homodimer
	in the hexagonal space group P6(1) to an R(cryst) of 20.5\%. The
	structure is similar in overall shape and fold to the previously
	determined subtype B, C and F PRs. The major differences lie in the
	conformation of the flap region. The flaps in the crystal structures
	of the unbound subtype B and C PRs, which were crystallized in tetragonal
	space groups, are either semi-open or wide open. In the present structure
	of subtype A PR the flaps are found in the closed position, a conformation
	that would be more anticipated in the structure of HIV protease complexed
	with an inhibitor. The amino-acid differences between the subtypes
	and their respective crystal space groups are discussed in terms
	of the differences in the flap conformations.},
  doi = {10.1107/S0907444909054298},
  institution = {Department of Biochemistry and Molecular Biology, University of Florida,
	Gainesville, FL 32610, USA.},
  keywords = {Amino Acid Sequence; Crystallography, X-Ray; HIV Protease; HIV-1;
	Models, Molecular; Molecular Sequence Data; Protein Folding; Protein
	Structure, Quaternary; Protein Structure, Tertiary; Sequence Alignment},
  owner = {emilio},
  pii = {S0907444909054298},
  pmid = {20179334},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1107/S0907444909054298}
}

@ARTICLE{Rocchia:Sridharan:Nicholls:Alexov:Chiabrera:Honig:2002,
  author = {Rocchia, W. and Sridharan, S. and Nicholls, A. and Alexov, Emil and
	Chiabrera, A. and Honig, B.},
  title = {Rapid grid-based construction of the molecular surface and the use
	of induced surface charge to calculate reaction field energies: Applications
	to the molecular systems and geometric objects},
  journal = {J. Comp. Chem.},
  year = {2002},
  volume = {23},
  pages = {128-137},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Roe:Okur:Wickstrom:Simmerling:2007,
  author = {Roe, Daniel R. and Okur, Asim and Wickstrom, Lauren and Hornak, Viktor
	and Simmerling, Carlos},
  title = {Secondary Structure Bias in Generalized Born Solvent Models:\
	Comparison of Conformational Ensembles and Free Energy of Solvent
	Polarization from Explicit and Implicit Solvation},
  journal = {The Journal of Physical Chemistry B},
  year = {2007},
  volume = {111},
  pages = {1846-1857},
  number = {7},
  doi = {10.1021/jp066831u},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp066831u},
  owner = {emilio},
  timestamp = {2011.01.18},
  url = {http://pubs.acs.org/doi/abs/10.1021/jp066831u}
}

@ARTICLE{Roitberg2007,
  author = {Adrian E Roitberg and Asim Okur and Carlos Simmerling},
  title = {Coupling of replica exchange simulations to a non-Boltzmann structure
	reservoir.},
  journal = {J Phys Chem B},
  year = {2007},
  volume = {111},
  pages = {2415--2418},
  number = {10},
  month = {Mar},
  abstract = {Computing converged ensemble properties remains challenging for large
	biomolecules. Replica exchange molecular dynamics (REMD) can significantly
	increase the efficiency of conformational sampling by using high
	temperatures to escape kinetic traps. Several groups, including ours,
	introduced the idea of coupling replica exchange to a pre-converged,
	Boltzmann-populated reservoir, usually at a temperature higher than
	that of the highest temperature replica. This procedure reduces computational
	cost because the long simulation times needed for extensive sampling
	are only carried out for a single temperature. However, a weakness
	of the approach is that the Boltzmann-weighted reservoir can still
	be difficult to generate. We now present the idea of employing a
	non-Boltzmann reservoir, whose structures can be generated through
	more efficient conformational sampling methods. We demonstrate that
	the approach is rigorous and derive a correct statistical mechanical
	exchange criterion between the reservoir and the replicas that drives
	Boltzmann-weighted probabilities for the replicas. We test this approach
	on the trpzip2 peptide and demonstrate that the resulting thermal
	stability profile is essentially indistinguishable from that obtained
	using very long (>100 ns) standard REMD simulations. The convergence
	of this reservoir-aided REMD is significantly faster than for regular
	REMD. Furthermore, we demonstrate that modification of the exchange
	criterion is essential; REMD simulations using a standard exchange
	function with the non-Boltzmann reservoir produced incorrect results.},
  doi = {10.1021/jp068335b},
  institution = {Quantum Theory Project, Department of Chemistry, University of Florida,
	Gainesville, Florida 32611, USA. roitberg@qtq.ufl.edu},
  keywords = {Computer Simulation; Models, Molecular; Peptides, chemistry; Protein
	Conformation; Protein Folding; Protein Structure, Secondary},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {17300191},
  timestamp = {2011.10.15},
  url = {http://dx.doi.org/10.1021/jp068335b}
}

@ARTICLE{Rosta2009,
  author = {Rosta, Edina and Woodcock, H. Lee and Brooks, Bernard R. and Hummer,
	Gerhard},
  title = {Artificial Reaction Coordinate "Tunneling" In Free Energy Calculations:
	Nucleic Acid Cleavage By Ribonuclease-H},
  journal = {Biophysical Journal},
  year = {2009},
  volume = {96},
  pages = {573a--573a},
  number = {3, Supplement 1},
  month = feb,
  issn = {0006-3495},
  owner = {emilio},
  timestamp = {2011.01.13},
  url = {http://www.sciencedirect.com/science/article/B94RW-4VK7BB2-3R7/2/577c0688fd9174bea810353d760e96e3}
}

@ARTICLE{Roux:Simonson:99,
  author = {Roux, B. and Simonson, T.},
  title = {Implicit Solvent Models},
  journal = {Biophys. Chem.},
  year = {1999},
  volume = {78},
  pages = {1-20},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Rowlinson:Widom:82,
  title = {Molecular Theory of Capillarity},
  publisher = {Oxford University Press},
  year = {1982},
  author = {Rowlinson, J. S. and Widom, B.},
  address = {Oxford},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Saito:92,
  author = {Saito, M.},
  journal = {Mol. Simul.},
  year = {1992},
  volume = {8},
  pages = {321-330},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Scarsi1999,
  author = {M. Scarsi and N. Majeux and A. Caflisch},
  title = {Hydrophobicity at the surface of proteins.},
  journal = {Proteins},
  year = {1999},
  volume = {37},
  pages = {565--575},
  number = {4},
  month = {Dec},
  abstract = {A new method is presented to quantitatively estimate and graphically
	display the propensity of nonpolar groups to bind at the surface
	of proteins. It is based on the calculation of the binding energy,
	i.e., van der Waals interaction plus protein electrostatic desolvation,
	of a nonpolar probe sphere rolled over the protein surface, and on
	the color coding of this quantity on a smooth molecular surface (hydrophobicity
	map). The method is validated on ten protein-ligand complexes and
	is shown to distinguish precisely where polar and nonpolar groups
	preferentially bind. Comparisons with existing approaches, like the
	display of the electrostatic potential or the curvature, illustrate
	the advantages and the better predictive power of the present method.
	Hydrophobicity maps will play an important role in the characterization
	of binding sites for the large number of proteins emerging from the
	genome projects and structure modeling approaches.},
  institution = {Department of Biochemistry, University of Zürich, Switzerland.},
  keywords = {Alkyl and Aryl Transferases; Annexin A2; Binding Sites; DNA; DNA-Binding
	Proteins; Dipeptides; Farnesyltranstransferase; Homeodomain Proteins;
	Macromolecular Substances; Models, Molecular; Nuclear Proteins; Peptides;
	Piperidines; Polyisoprenyl Phosphates; Protein Binding; Protein Conformation;
	Protein Structure, Quaternary; Proteins; Proto-Oncogene Proteins;
	Proto-Oncogene Proteins c-mdm2; S100 Proteins; Sesquiterpenes; Static
	Electricity; Surface Properties; Thermodynamics; Thrombin; Tumor
	Suppressor Protein p53},
  owner = {emilio},
  pii = {3.0.CO;2-V},
  pmid = {10651272},
  timestamp = {2010.04.22}
}

@ARTICLE{Schaefer:Bartels:Karplus:98,
  author = {Schaefer, M. and Bartels, C. and Karplus, M.},
  title = {Solution Conformations and Thermodynamics of Structured Peptides:
	Molecular Dynamics Simulations with Explicit Solvent},
  journal = {J. Mol. Biol.},
  year = {1998},
  volume = {284},
  pages = {835-848},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Schaefer:Bartels:Leclerc:Karplus:2001,
  author = {Schaefer, M. and Bartels, C. and Leclerc, F. and Karplus, M.},
  title = {Effective atom volumes for implicit solvent models: comparison between
	Voronoi volumes and minimum fluctuation volumes},
  journal = {J. Comp. Chem.},
  year = {2001},
  volume = {22},
  pages = {1857--1879},
  owner = {emilio},
  timestamp = {2010.11.01}
}

@ARTICLE{Schaefer:Froemmel:90,
  author = {Schaefer, M. and Froemmel, C.},
  title = {A Precise Analytical Method for Calculating the Electrostatic Energy
	of Macromolecules in Aqueous Solution},
  journal = {J. Mol. Biol.},
  year = {1990},
  volume = {216},
  pages = {1045-1066},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Schaefer:Karplus:96,
  author = {Schaefer, M. and Karplus, M.},
  title = {A Comprehensive Analytical Treatment of Continuum Electrostatic},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {1578-1599},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Scheraga2007,
  author = {Harold A Scheraga and Mey Khalili and Adam Liwo},
  title = {Protein-folding dynamics: overview of molecular simulation techniques.},
  journal = {Annu. Rev. Phys. Chem.},
  year = {2007},
  volume = {58},
  pages = {57--83},
  abstract = {Molecular dynamics (MD) is an invaluable tool with which to study
	protein folding in silico. Although just a few years ago the dynamic
	behavior of a protein molecule could be simulated only in the neighborhood
	of the experimental conformation (or protein unfolding could be simulated
	at high temperature), the advent of distributed computing, new techniques
	such as replica-exchange MD, new approaches (based on, e.g., the
	stochastic difference equation), and physics-based reduced models
	of proteins now make it possible to study protein-folding pathways
	from completely unfolded structures. In this review, we present algorithms
	for MD and their extensions and applications to protein-folding studies,
	using all-atom models with explicit and implicit solvent as well
	as reduced models of polypeptide chains.},
  doi = {10.1146/annurev.physchem.58.032806.104614},
  institution = {rnell University, Ithaca, NY 14853-1301, USA. has5@cornell.edu},
  keywords = {Algorithms; Animals; Computer Simulation; Hydrogen-Ion Concentration;
	Models, Molecular; Protein Folding; Proteins},
  owner = {emilio},
  pmid = {17034338},
  timestamp = {2010.05.06},
  url = {http://dx.doi.org/10.1146/annurev.physchem.58.032806.104614}
}

@ARTICLE{Schleinkofer2005,
  author = {Karin Schleinkofer and Sudarko and Peter J Winn and Susanne K Lüdemann
	and Rebecca C Wade},
  title = {Do mammalian cytochrome P450s show multiple ligand access pathways
	and ligand channelling?},
  journal = {EMBO Rep},
  year = {2005},
  volume = {6},
  pages = {584--589},
  number = {6},
  month = {Jun},
  abstract = {Understanding substrate binding and product release in cytochrome
	P450 (CYP) enzymes is important for explaining their key role in
	drug metabolism, toxicity, xenobiotic degradation and biosynthesis.
	Here, molecular simulations of substrate and product exit from the
	buried active site of a mammalian P450, the microsomal CYP2C5, identified
	a dominant exit channel, termed pathway (pw) 2c. Previous simulations
	with soluble bacterial P450s showed a different dominant egress channel,
	pw2a. Combining these, we propose two mechanisms in CYP2C5: (i) a
	one-way route by which lipophilic substrates access the enzyme from
	the membrane by pw2a and hydroxylated products egress along pw2c;
	and (ii) a two-way route for access and egress, along pw2c, for soluble
	compounds. The proposed differences in substrate access and product
	egress routes between membrane-bound mammalian P450s and soluble
	bacterial P450s highlight the adaptability of the P450 fold to the
	requirements of differing cellular locations and substrate specificity
	profiles.},
  institution = {EML Research gGmbH, Villa Bosch, Schloss-Wolfsbrunnenweg 33, 69118
	Heidelberg, Germany},
  keywords = {Animals; Computer Simulation; Cytochrome P-450 Enzyme System; Desoxycorticosterone;
	Ligands; Mammals; Models, Molecular; Progesterone; Protein Binding;
	Steroid 21-Hydroxylase; Substrate Specificity},
  owner = {emilio},
  pmid = {16028306},
  timestamp = {2010.09.07}
}

@ARTICLE{Schlick:97,
  author = {Schlick, T. and Poarth, E. and Mandziuk, M.},
  journal = {Ann. Rev. Biophys. Biomol. Struct.},
  year = {1996},
  volume = {26},
  pages = {181-222},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Schmidt:Lee:91,
  author = {Schmidt, K. A. and Lee, M. A.},
  journal = {J. Stat. Phys.},
  year = {1991},
  volume = {63},
  pages = {1223-1231},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Schuler2001,
  author = {Schuler, Lukas D. and Daura, Xavier and van Gunsteren, Wilfred F.},
  title = {An improved GROMOS96 force field for aliphatic hydrocarbons in the
	condensed phase},
  journal = {J. Comput. Chem.},
  year = {2001},
  volume = {22},
  pages = {1205--1218},
  number = {11},
  abstract = {Abstract 10.1002/jcc.1078.abs Over the past 4 years the GROMOS96 force
	field has been successfully used in biomolecular simulations, for
	example in peptide folding studies and detailed protein investigations,
	but no applications to lipid systems have been published yet. Here
	we provide a detailed investigation of aliphatic liquid systems.
	For liquids of larger aliphatic chains, n-heptane and longer, the
	standard GROMOS96 parameter sets 43A1 and 43A2 yield a too low pressure
	at the experimental density. Therefore, a reparametrization of the
	GROMOS96 force field regarding aliphatic carbons was initiated. The
	new force field parameter set 45A3 shows considerable improvements
	for n-alkanes, cyclo-, iso-, and neoalkanes and other branched aliphatics.
	Liquid densities and heat of vaporization are reproduced for almost
	all of these molecules. Excellent agreement is found with experiment
	for the free energy of hydration for alkanes. The GROMOS96 45A3 parameter
	set should, therefore, be suitable for application to lipid aggregates
	such as membranes and micelles, for mixed systems of aliphatics with
	or without water, for polymers, and other apolar systems that may
	interact with different biomolecules. © 2001 John Wiley & Sons, Inc.
	J Comput Chem 22: 1205–1218, 2001},
  issn = {1096-987X},
  keywords = {GROMOS96 force field 45A3, aliphatic hydrocarbons, condensed phase
	properties, molecular dynamics simulation},
  owner = {emilio},
  publisher = {John Wiley \& Sons, Inc.},
  timestamp = {2011.02.07},
  url = {http://dx.doi.org/10.1002/jcc.1078}
}

@ARTICLE{Schwarzl:Tschopp:Smith:Fisher:2002,
  author = {Schwarzl, S. M. and Tschopp, T. B. and Smith, J. C. and Fisher, S.},
  title = {Can the Calculation of Ligand Binding Free Energies be Improved with
	Continuum Solvent Electrostatics and an Ideal-Gas Entropy Correction},
  journal = {J. Comp. Chem.},
  year = {2002},
  volume = {23},
  pages = {1143-1149},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Searle:92,
  author = {Searle, M. S. and Williams, D. H. and Gerhard, U.},
  title = {Partitioning of Free Energy Contributions in the Estimation of Binding
	Constants: Residual Motions and Consequences for Amide-Amide Hydrogen
	Bond Strengths},
  journal = {J. Am. Chem. Soc.},
  year = {1992},
  volume = {114},
  pages = {10697-10704},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Serdyuk2007,
  title = {Methods in Molecular Biophysics: Structure, Dynamics, Function},
  publisher = {Cambridge University Press},
  year = {2007},
  author = {Igor N. Serdyuk and Nathan R. Zaccai and Giuseppe Zaccai},
  address = {Cambridge ; New York},
  owner = {emilio},
  timestamp = {2011.02.08}
}

@ARTICLE{Setny2010,
  author = {Piotr Setny and Riccardo Baron and J. Andrew McCammon},
  title = {How Can Hydrophobic Association Be Enthalpy Driven?},
  journal = {J Chem Theory Comput},
  year = {2010},
  volume = {6},
  pages = {2866--2871},
  number = {9},
  month = {Sep},
  abstract = {Hydrophobic association is often recognized as being driven by favorable
	entropic contributions. Here, using explicit solvent molecular dynamics
	simulations we investigate binding in a model hydrophobic receptor-ligand
	system which appears, instead, to be driven by enthalpy and opposed
	by entropy. We use the temperature dependence of the potential of
	mean force to analyze the thermodynamic contributions along the association
	coordinate. Relating such contributions to the ongoing changes in
	system hydration allows us to demonstrate that the overall binding
	thermodynamics is determined by the expulsion of disorganized water
	from the receptor cavity. Our model study sheds light on the solvent-induced
	driving forces for receptor-ligand association of general, transferable
	relevance for biological systems with poorly hydrated binding sites.},
  doi = {10.1021/ct1003077},
  institution = {Department of Chemistry and Biochemistry, Center for Theoretical
	Biological Physics, Howard Hughes Medical Institute, Department of
	Pharmacology, University of California, San Diego and Physics Department,
	Technical University Munich, 85748 Garching, Germany.},
  owner = {emilio},
  pmid = {20844599},
  timestamp = {2010.09.23},
  url = {http://dx.doi.org/10.1021/ct1003077}
}

@ARTICLE{Sham:97,
  author = {Sham, Y. and Chu, Z. T. and Warshel, A.},
  journal = {J. Phys. Chem. B},
  year = {1997},
  volume = {101},
  pages = {4458-4472},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Sham:98,
  author = {Sham, Y. and Muegge, I. and Warshel, A.},
  journal = {Biophys. J.},
  year = {in press},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Sham:Chu:Tao:Warshel:2000,
  author = {Sham, {Y. Y.} and Chu, {Z. T.} and Tao, H. and Warshel, A.},
  title = {Examining Methods for Calculations of Binding Free Energies: {LRA},
	{LIE}, {PDLD-LRA}, and {PDLD/S-LRA} Calculations of Ligands Binding
	to an HIV Protease},
  journal = {Prot. Struct. Funct. Genet.},
  year = {2000},
  volume = {39},
  pages = {393--407},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Shan2011,
  author = {Yibing Shan and Eric T Kim and Michael P Eastwood and Ron O Dror
	and Markus A Seeliger and David E Shaw},
  title = {How does a drug molecule find its target binding site?},
  journal = {J Am Chem Soc},
  year = {2011},
  volume = {133},
  pages = {9181--9183},
  number = {24},
  month = {Jun},
  doi = {10.1021/ja202726y},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {21545110},
  timestamp = {2011.07.15},
  url = {http://dx.doi.org/10.1021/ja202726y}
}

@ARTICLE{Sharp:91,
  author = {Sharp, K. and Nicholls, A. and Fine, R. and Honig, B.},
  journal = {Science},
  year = {1991},
  volume = {252},
  pages = {106-109},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Shaw2010,
  author = {David E Shaw and Paul Maragakis and Kresten Lindorff-Larsen and Stefano
	Piana and Ron O Dror and Michael P Eastwood and Joseph A Bank and
	John M Jumper and John K Salmon and Yibing Shan and Willy Wriggers},
  title = {Atomic-level characterization of the structural dynamics of proteins.},
  journal = {Science},
  year = {2010},
  volume = {330},
  pages = {341--346},
  number = {6002},
  month = {Oct},
  abstract = {Molecular dynamics (MD) simulations are widely used to study protein
	motions at an atomic level of detail, but they have been limited
	to time scales shorter than those of many biologically critical conformational
	changes. We examined two fundamental processes in protein dynamics--protein
	folding and conformational change within the folded state--by means
	of extremely long all-atom MD simulations conducted on a special-purpose
	machine. Equilibrium simulations of a WW protein domain captured
	multiple folding and unfolding events that consistently follow a
	well-defined folding pathway; separate simulations of the protein's
	constituent substructures shed light on possible determinants of
	this pathway. A 1-millisecond simulation of the folded protein BPTI
	reveals a small number of structurally distinct conformational states
	whose reversible interconversion is slower than local relaxations
	within those states by a factor of more than 1000.},
  doi = {10.1126/science.1187409},
  institution = {D. E. Shaw Research, 120 West 45th Street, New York, NY 10036, USA.
	David.Shaw@DEShawResearch.com},
  keywords = {Amino Acid Substitution; Aprotinin; Computational Biology; Computers;
	Kinetics; Microfilament Proteins; Models, Molecular; Molecular Dynamics
	Simulation; Mutant Proteins; Protein Conformation; Protein Folding;
	Protein Structure, Tertiary; Proteins; Solvents; Thermodynamics},
  owner = {emilio},
  pii = {330/6002/341},
  pmid = {20947758},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1126/science.1187409}
}

@ARTICLE{Sherman2006,
  author = {Woody Sherman and Tyler Day and Matthew P Jacobson and Richard A
	Friesner and Ramy Farid},
  title = {Novel procedure for modeling ligand/receptor induced fit effects.},
  journal = {J. Med. Chem.},
  year = {2006},
  volume = {49},
  pages = {534--553},
  number = {2},
  month = {Jan},
  abstract = {We present a novel protein-ligand docking method that accurately accounts
	for both ligand and receptor flexibility by iteratively combining
	rigid receptor docking (Glide) with protein structure prediction
	(Prime) techniques. While traditional rigid-receptor docking methods
	are useful when the receptor structure does not change substantially
	upon ligand binding, success is limited when the protein must be
	"induced" into the correct binding conformation for a given ligand.
	We provide an in-depth description of our novel methodology and present
	results for 21 pharmaceutically relevant examples. Traditional rigid-receptor
	docking for these 21 cases yields an average RMSD of 5.5 A. The average
	ligand RMSD for docking to a flexible receptor for the 21 pairs is
	1.4 A; the RMSD is < or =1.8 A for 18 of the cases. For the three
	cases with RMSDs greater than 1.8 A, the core of the ligand is properly
	docked and all key protein/ligand interactions are captured.},
  doi = {10.1021/jm050540c},
  institution = {Schrödinger, Inc., New York, New York 10036, USA.},
  keywords = {Binding Sites; Ligands; Mathematical Computing; Models, Molecular;
	Protein Binding; Protein Conformation; Proteins; Quantitative Structure-Activity
	Relationsh; ip},
  owner = {emilio},
  pmid = {16420040},
  timestamp = {2010.05.27},
  url = {http://dx.doi.org/10.1021/jm050540c}
}

@ARTICLE{Shi2009a,
  author = {Rong Shi and Ariane Proteau and John Wagner and Qizhi Cui and Enrico
	O Purisima and Allan Matte and Miroslaw Cygler},
  title = {Trapping open and closed forms of FitE: a group III periplasmic binding
	protein.},
  journal = {Proteins},
  year = {2009},
  volume = {75},
  pages = {598--609},
  number = {3},
  month = {May},
  abstract = {Periplasmic binding proteins (PBPs) are essential components of bacterial
	transport systems, necessary for bacterial growth and survival. The
	two-domain structures of PBPs are topologically classified into three
	groups based on the number of crossovers or hinges between the globular
	domains: group I PBPs have three connections, group II have two,
	and group III have only one. Although a large number of structures
	for group I or II PBPs are known, fewer group III PBPs have been
	structurally characterized. Group I and II PBPs exhibit significant
	domain motions during transition from the unbound to ligand-bound
	form, however, no large conformational changes have been observed
	to date in group III PBPs. We have solved the crystal structure of
	a periplasmic binding protein FitE, part of an iron transport system,
	fit, recently identified in a clinical E. coli isolate. The structure,
	determined at 1.8 A resolution, shows that FitE is a group III PBP
	containing a single alpha-helix bridging the two domains. Among the
	individual FitE molecules present in two crystal forms we observed
	three different conformations (open, closed, intermediate). Our crystallographic
	and molecular dynamics results strongly support the notion that group
	III PBPs also adopt the same Venus flytrap mechanism as do groups
	I and II PBPs. Unlike other group III PBPs, FitE forms dimers both
	in solution and in the crystals. The putative siderophore binding
	pocket is lined with arginine residues, suggesting an anionic nature
	of the iron-containing siderophore.},
  doi = {10.1002/prot.22272},
  institution = {Department of Biochemistry, McGill University, Montréal, Québec,
	Canada.},
  keywords = {ATP-Binding Cassette Transporters; Binding Sites; Computer Simulation;
	Crystallography, X-Ray; Dimerization; Electrophoresis, Polyacrylamide
	Gel; Escherichia coli O157; Escherichia coli Proteins; Models, Molecular;
	Periplasmic Binding Proteins; Protein Conformation; Protein Structure,
	Secondary; Protein Structure, Tertiary; Spectrometry, Mass, Electrospray
	Ionization},
  owner = {emilio},
  pmid = {19004000},
  timestamp = {2010.05.20},
  url = {http://dx.doi.org/10.1002/prot.22272}
}

@ARTICLE{Shi2009,
  author = {Shi, Yemin and Liu, Hanbin and Gai, Dahai and Ma, Jianpeng and Chen,
	Xiaojiang S.},
  title = {A Computational Analysis of {ATP} Binding of {SV40} Large Tumor Antigen
	Helicase Motor},
  journal = {PLoS Comput Biol},
  year = {2009},
  volume = {5},
  pages = {e1000514--},
  number = {9},
  month = sep,
  abstract = {<title>Author Summary</title> <p>The Large Tumor antigen (LTag) encoded
	by Simian Virus 40 (SV40) is a marvelous molecule that is not only
	a viral oncogene, but also an efficient molecular machine as a helicase
	that unwinds double helix DNA for genome replication, an essential
	process in all living organisms. LTag hexameric helicase uses the
	energy of ATP to power its conformational switch for DNA unwinding.
	Understanding how the LTag conformational switch is coupled to the
	energy from ATP usage

license: MIT

license_type: permissive

branch_name: refs/heads/master

gha_license_id: MIT

gha_language: TeX

extension: bib