text:
by LTag to do the mechanical work of unwinding
	DNA is of great interest to biologists, and yet remains to be established.
	Based on our previous high-resolution structures of LTag helicase
	in different conformational states, we simulated an LTag conformational
	transition pathway in the ATP binding process using the targeted
	molecular dynamics method. Our simulation results suggest a three-step
	process for the ATP binding to the nucleotide pocket, in which ATP
	is eventually “locked” into the pocket by three pairs of “locker”
	interactions. We have also quantitatively evaluated the energy profile
	of ATP binding using a special computational simulation technique.
	Additionally, our simulation study of ATP binding by LTag and the
	accompanying conformational switches in the context of a hexamer
	leads to a refined cooperative iris model that may be used for DNA
	unwinding.</p>},
  owner = {emilio},
  publisher = {Public Library of Science},
  timestamp = {2010.10.08},
  url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1000514}
}

@INBOOK{Shirts:Mobley:Brown:2010:ChapterBook,
  chapter = {Free energy calculations in structure-based drug design},
  title = {Structure Based Drug Discovery},
  publisher = {Cambridge University Press},
  year = {2010},
  editor = {K.M. Merz and D. Ringe and C.H. Reynolds},
  author = {Shirts, M.R. and Mobley, D.L. and Brown, S.P.},
  owner = {emilio},
  timestamp = {2010.04.20}
}

@ARTICLE{Shirts:Mobley:Chodera:2007:review,
  author = {Shirts, M.R. and Mobley, D.L. and Chodera, J.D.},
  title = {Alchemical free energy calculations: ready for prime time?},
  journal = {Ann. Rep. Comput. Chem.},
  year = {2007},
  volume = {3},
  pages = {41-59},
  owner = {emilio},
  timestamp = {2010.04.21}
}

@ARTICLE{Shirts:Bair:Hooker:Pande:2003,
  author = {Shirts, Michael R. and Bair, Eric and Hooker, Giles and Pande, Vijay
	S.},
  title = {Equilibrium Free Energies from Nonequilibrium Measurements Using
	Maximum-Likelihood Methods},
  journal = {Phys. Rev. Lett.},
  year = {2003},
  volume = {91},
  pages = {140601},
  number = {14},
  month = {Oct},
  doi = {10.1103/PhysRevLett.91.140601},
  numpages = {4},
  owner = {emilio},
  publisher = {American Physical Society},
  timestamp = {2010.04.30}
}

@ARTICLE{Shirts2008a,
  author = {Michael R Shirts and John D Chodera},
  title = {Statistically optimal analysis of samples from multiple equilibrium
	states.},
  journal = {J. Chem. Phys.},
  year = {2008},
  volume = {129},
  pages = {124105},
  number = {12},
  month = {Sep},
  abstract = {We present a new estimator for computing free energy differences and
	thermodynamic expectations as well as their uncertainties from samples
	obtained from multiple equilibrium states via either simulation or
	experiment. The estimator, which we call the multistate Bennett acceptance
	ratio estimator (MBAR) because it reduces to the Bennett acceptance
	ratio estimator (BAR) when only two states are considered, has significant
	advantages over multiple histogram reweighting methods for combining
	data from multiple states. It does not require the sampled energy
	range to be discretized to produce histograms, eliminating bias due
	to energy binning and significantly reducing the time complexity
	of computing a solution to the estimating equations in many cases.
	Additionally, an estimate of the statistical uncertainty is provided
	for all estimated quantities. In the large sample limit, MBAR is
	unbiased and has the lowest variance of any known estimator for making
	use of equilibrium data collected from multiple states. We illustrate
	this method by producing a highly precise estimate of the potential
	of mean force for a DNA hairpin system, combining data from multiple
	optical tweezer measurements under constant force bias.},
  doi = {10.1063/1.2978177},
  institution = {Department of Chemical Engineering, University of Virginia, Charlottesville,
	Virginia 22904, USA. michael.shirts@virginia.edu},
  keywords = {DNA; Data Interpretation, Statistical; Laboratories; Thermodynamics;
	Uncertainty},
  owner = {emilio},
  pmid = {19045004},
  timestamp = {2010.04.29},
  url = {http://dx.doi.org/10.1063/1.2978177}
}

@INBOOK{Shirts:Mobley:Brown:BookChapter2010,
  chapter = {Free-energy calculations in structure-based drug design},
  pages = {61--86},
  title = {Drug Design -- Structure- and Ligand-Based Approaches},
  publisher = {Cambridge University Press},
  year = {2010},
  editor = {Kenneth M. Merz Jr., Dagmar Ringe and Charles H. Reynolds},
  author = {Michael R. Shirts and David L. Mobley and Scott P. Brown},
  owner = {emilio},
  timestamp = {2010.10.11}
}

@ARTICLE{Shirts2007,
  author = {Michael R Shirts and David L Mobley and John D Chodera and Vijay
	S Pande},
  title = {Accurate and efficient corrections for missing dispersion interactions
	in molecular simulations.},
  journal = {J Phys Chem B},
  year = {2007},
  volume = {111},
  pages = {13052--13063},
  number = {45},
  month = {Nov},
  abstract = {In simulations, molecular dispersion interactions are frequently neglected
	beyond a cutoff of around 1 nm. In some cases, analytical corrections
	appropriate for isotropic systems are applied to the pressure and/or
	the potential energy. Here, we show that in systems containing macromolecules,
	either of these approaches introduce statistically significant errors
	in some observed properties; for example, the choice of cutoff can
	affect computed free energies of ligand binding to proteins by 1
	to 2 kcal/mol. We review current methods for eliminating this cutoff-dependent
	behavior of the dispersion energy and identify some situations where
	they fail. We introduce two new formalisms, appropriate for binding
	free energy calculations, which overcome these failings, requiring
	minimal computational effort beyond the time required to run the
	original simulation. When these cutoff approximations are applied,
	which can be done after all simulations are completed, results are
	consistent across simulations run with different cutoffs. In many
	situations, simulations can be run with even shorter cutoffs than
	typically used, resulting in increased computational efficiency.},
  doi = {10.1021/jp0735987},
  institution = {Department of Chemistry, Columbia University, New York, New York
	10027, USA. michael.shirts@columbia.edu},
  keywords = {Computer Simulation; Ligands; Models, Chemical; Protein Binding; Solvents;
	Tacrolimus; Tacrolimus Binding Protein 1A; Thermodynamics},
  owner = {emilio},
  pmid = {17949030},
  timestamp = {2010.04.29},
  url = {http://dx.doi.org/10.1021/jp0735987}
}

@ARTICLE{Shirts2005,
  author = {Michael R Shirts and Vijay S Pande},
  title = {Comparison of efficiency and bias of free energies computed by exponential
	averaging, the Bennett acceptance ratio, and thermodynamic integration.},
  journal = {J Chem Phys},
  year = {2005},
  volume = {122},
  pages = {144107},
  number = {14},
  month = {Apr},
  abstract = {Recent work has demonstrated the Bennett acceptance ratio method is
	the best asymptotically unbiased method for determining the equilibrium
	free energy between two end states given work distributions collected
	from either equilibrium and nonequilibrium data. However, it is still
	not clear what the practical advantage of this acceptance ratio method
	is over other common methods in atomistic simulations. In this study,
	we first review theoretical estimates of the bias and variance of
	exponential averaging (EXP), thermodynamic integration (TI), and
	the Bennett acceptance ratio (BAR). In the process, we present a
	new simple scheme for computing the variance and bias of many estimators,
	and demonstrate the connections between BAR and the weighted histogram
	analysis method. Next, a series of analytically solvable toy problems
	is examined to shed more light on the relative performance in terms
	of the bias and efficiency of these three methods. Interestingly,
	it is impossible to conclusively identify a "best" method for calculating
	the free energy, as each of the three methods performs more efficiently
	than the others in at least one situation examined in these toy problems.
	Finally, sample problems of the insertion/deletion of both a Lennard-Jones
	particle and a much larger molecule in TIP3P water are examined by
	these three methods. In all tests of atomistic systems, free energies
	obtained with BAR have significantly lower bias and smaller variance
	than when using EXP or TI, especially when the overlap in phase space
	between end states is small. For example, BAR can extract as much
	information from multiple fast, far-from-equilibrium simulations
	as from fewer simulations near equilibrium, which EXP cannot. Although
	TI and sometimes even EXP can be somewhat more efficient in idealized
	toy problems, in the realistic atomistic situations tested in this
	paper, BAR is significantly more efficient than all other methods.},
  doi = {10.1063/1.1873592},
  institution = {Department of Chemistry, Stanford University, Stanford, California
	94305-5080, USA.},
  keywords = {Bias (Epidemiology); Computer Simulation; Energy Transfer; Models,
	Theoretical; Thermodynamics},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {15847516},
  timestamp = {2011.11.06},
  url = {http://dx.doi.org/10.1063/1.1873592}
}

@ARTICLE{Shirts:Pande:2005,
  author = {Michael R. Shirts and Vijay S. Pande},
  title = {Solvation free energies of amino acid side chain analogs for common
	molecular mechanics water models},
  journal = {J. Chem. Phys.},
  year = {2005},
  volume = {122},
  pages = {134508},
  number = {13},
  eid = {134508},
  doi = {10.1063/1.1877132},
  keywords = {solvation; free energy; water; proteins},
  numpages = {13},
  owner = {emilio},
  publisher = {AIP},
  timestamp = {2011.01.18},
  url = {http://link.aip.org/link/?JCP/122/134508/1}
}

@ARTICLE{Shoichet2004,
  author = {Brian K Shoichet},
  title = {Virtual screening of chemical libraries.},
  journal = {Nature},
  year = {2004},
  volume = {432},
  pages = {862--865},
  number = {7019},
  month = {Dec},
  abstract = {Virtual screening uses computer-based methods to discover new ligands
	on the basis of biological structures. Although widely heralded in
	the 1970s and 1980s, the technique has since struggled to meet its
	initial promise, and drug discovery remains dominated by empirical
	screening. Recent successes in predicting new ligands and their receptor-bound
	structures, and better rates of ligand discovery compared to empirical
	screening, have re-ignited interest in virtual screening, which is
	now widely used in drug discovery, albeit on a more limited scale
	than empirical screening.},
  doi = {10.1038/nature03197},
  institution = {Department of Pharmaceutical Chemistry, University of California,
	600 16th Street, San Francisco, California 94143-2240, USA. shoichet@cgl.ucsf.edu},
  keywords = {Computer Simulation; Drug Evaluation, Preclinical; Ligands; Models,
	Molecular; Molecular Conformation; Pharmaceutical Preparations},
  owner = {emilio},
  pii = {nature03197},
  pmid = {15602552},
  timestamp = {2010.10.27},
  url = {http://dx.doi.org/10.1038/nature03197}
}

@ARTICLE{Shoichet1999,
  author = {B. K. Shoichet and A. R. Leach and I. D. Kuntz},
  title = {Ligand solvation in molecular docking.},
  journal = {Proteins},
  year = {1999},
  volume = {34},
  pages = {4--16},
  number = {1},
  month = {Jan},
  abstract = {Solvation plays an important role in ligand-protein association and
	has a strong impact on comparisons of binding energies for dissimilar
	molecules. When databases of such molecules are screened for complementarity
	to receptors of known structure, as often occurs in structure-based
	inhibitor discovery, failure to consider ligand solvation often leads
	to putative ligands that are too highly charged or too large. To
	correct for the different charge states and sizes of the ligands,
	we calculated electrostatic and non-polar solvation free energies
	for molecules in a widely used molecular database, the Available
	Chemicals Directory (ACD). A modified Born equation treatment was
	used to calculate the electrostatic component of ligand solvation.
	The non-polar component of ligand solvation was calculated based
	on the surface area of the ligand and parameters derived from the
	hydration energies of apolar ligands. These solvation energies were
	subtracted from the ligand-receptor interaction energies. We tested
	the usefulness of these corrections by screening the ACD for molecules
	that complemented three proteins of known structure, using a molecular
	docking program. Correcting for ligand solvation improved the rankings
	of known ligands and discriminated against molecules with inappropriate
	charge states and sizes.},
  institution = {Department of Molecular Pharmacology and Biological Chemistry, Northwestern
	University Medical School, Chicago, Illinois 60611-3008, USA. b-shoichet@nwu.edu},
  keywords = {Aniline Compounds; Binding Sites; Computer Simulation; Databases,
	Factual; Indoles; Kinetics; Ligands; Lysosomes; Models, Molecular;
	Protein Binding; Pteridines; Tetrahydrofolate Dehydrogenase; Thymidine
	Monophosphate},
  owner = {emilio},
  pii = {3.0.CO;2-6},
  pmid = {10336382},
  timestamp = {2010.04.22}
}

@ARTICLE{Shoichet2002a,
  author = {Brian K Shoichet and Susan L McGovern and Binqing Wei and John J
	Irwin},
  title = {Lead discovery using molecular docking.},
  journal = {Curr. Opin. Chem. Biol.},
  year = {2002},
  volume = {6},
  pages = {439--446},
  number = {4},
  month = {Aug},
  abstract = {As the structures of more and more proteins and nucleic acids become
	available, molecular docking is increasingly considered for lead
	discovery. Recent studies consider the hit-rate enhancement of docking
	screens and the accuracy of docking structure predictions. As more
	structures are determined experimentally, docking against homology-modeled
	targets also becomes possible for more proteins. With more docking
	studies being undertaken, the 'drug-likeness' and specificity of
	docking hits is also being examined.},
  institution = {Department of Molecular Pharmacology and Biological Chemistry, Northwestern
	University, 303 East Chicago Avenue, Chicago, IL 60611-3008, USA.
	b-shoichet@northwestern.edu},
  keywords = {Animals; Computer Simulation; Drug Delivery Systems; Drug Design;
	Humans; Models, Molecular; Protein Binding},
  owner = {emilio},
  pii = {S1367593102003393},
  pmid = {12133718},
  timestamp = {2010.10.27}
}

@ARTICLE{Siebert:Hummer:2002,
  author = {Siebert, X. and Hummer, G.},
  title = {Hydrophobicity Maps of the N-Peptide Coiled Coil of HIV-1 gp41},
  journal = {Biochemistry},
  year = {2002},
  volume = {41},
  pages = {2965-2961},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Simons:Bonneau:Ruczinski:Baker:99,
  author = {Simons, K. T. and Bonneau, R. and Ruczinski, I. and Baker, D.},
  title = {Ab inition protein structure prediction of {CASP} {III} targets using
	{ROSETTA}},
  journal = {Proteins: Struct. Funct. Genet.},
  year = {1999},
  volume = {S3},
  pages = {171-176},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Simonsen:Brooks:96,
  author = {Simonsen, T. and Brooks, C. L.},
  journal = {J. Am. Chem. Soc.},
  year = {1996},
  volume = {118},
  pages = {8452-8458},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Simonsen:Perahia:95,
  author = {Simonsen, T. and Perahia, D.},
  journal = {J. Am. Chem. Soc.},
  year = {1995},
  volume = {117},
  pages = {7987-8000},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Simonson:2001,
  author = {Simonson, T.},
  title = {Macromolecular electrostatics: continuum models and their growing
	pains},
  journal = {Curr. Op. Struc. Biol.},
  year = {2001},
  volume = {11},
  pages = {243-252},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Simonson:99,
  author = {Simonson, T.},
  title = {Dielectric Relaxation in Proteins: Microscopic and macroscopic Models},
  journal = {International Jrnl. of Quantum Chemistry},
  year = {1999},
  volume = {73},
  pages = {45-57},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Simonson:97,
  author = {Simonson, T. and Archentis, G. and Karplus, M.},
  journal = {J. Phys. Chem. B},
  year = {1997},
  volume = {101},
  pages = {8349-8362},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Simonson2002,
  author = {Thomas Simonson and Georgios Archontis and Martin Karplus},
  title = {Free energy simulations come of age: protein-ligand recognition.},
  journal = {Acc. Chem. Res.},
  year = {2002},
  volume = {35},
  pages = {430--437},
  number = {6},
  month = {Jun},
  abstract = {In recent years, molecular dynamics simulations of biomolecular free
	energy differences have benefited from significant methodological
	advances and increased computer power. Applications to molecular
	recognition provide an understanding of the interactions involved
	that goes beyond, and is an important complement to, experimental
	studies. Poisson-Boltzmann electrostatic models provide a faster
	and simpler free energy method in cases where electrostatic interactions
	are important. We illustrate both molecular dynamics and Poisson-Boltzmann
	methods with a detailed study of amino acid recognition by aspartyl-tRNA
	synthetase, whose specificity is important for maintaining the integrity
	of the genetic code.},
  doi = {10.1021/ar010030m},
  institution = {Laboratoire de Biologie et G'enomique Structurales (CNRS), IGBMC,
	1 rue Laurent Fries, 67404 Illkirch-Strasbourg, France.},
  keywords = {Computer Simulation; Ligands; Protein Binding; Proteins; Static Electricity;
	Thermodynamics},
  owner = {emilio},
  pii = {ar010030m},
  pmid = {12069628},
  timestamp = {2010.04.30}
}

@ARTICLE{Simonson:Brunger:94,
  author = {Simonson, T. and Br\"{u}nger, A. T. },
  title = {Solvation free-energies estimated from macroscopic continuum theory
	- an accuracy assessment},
  journal = {J. Phys. Chem.},
  year = {1994},
  volume = {98},
  pages = {4683-4694},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Singh2010,
  author = {Nidhi Singh and Arieh Warshel},
  title = {Absolute binding free energy calculations: on the accuracy of computational
	scoring of protein-ligand interactions.},
  journal = {Proteins},
  year = {2010},
  volume = {78},
  pages = {1705--1723},
  number = {7},
  month = {May},
  abstract = {Calculating the absolute binding free energies is a challenging task.
	Reliable estimates of binding free energies should provide a guide
	for rational drug design. It should also provide us with deeper understanding
	of the correlation between protein structure and its function. Further
	applications may include identifying novel molecular scaffolds and
	optimizing lead compounds in computer-aided drug design. Available
	options to evaluate the absolute binding free energies range from
	the rigorous but expensive free energy perturbation to the microscopic
	linear response approximation (LRA/beta version) and related approaches
	including the linear interaction energy (LIE) to the more approximated
	and considerably faster scaled protein dipoles Langevin dipoles (PDLD/S-LRA
	version) as well as the less rigorous molecular mechanics Poisson-Boltzmann/surface
	area (MM/PBSA) and generalized born/surface area (MM/GBSA) to the
	less accurate scoring functions. There is a need for an assessment
	of the performance of different approaches in terms of computer time
	and reliability. We present a comparative study of the LRA/beta,
	the LIE, the PDLD/S-LRA/beta, and the more widely used MM/PBSA and
	assess their abilities to estimate the absolute binding energies.
	The LRA and LIE methods perform reasonably well but require specialized
	parameterization for the nonelectrostatic term. The PDLD/S-LRA/beta
	performs effectively without the need of reparameterization. Our
	assessment of the MM/PBSA is less optimistic. This approach appears
	to provide erroneous estimates of the absolute binding energies because
	of its incorrect entropies and the problematic treatment of electrostatic
	energies. Overall, the PDLD/S-LRA/beta appears to offer an appealing
	option for the final stages of massive screening approaches.},
  doi = {10.1002/prot.22687},
  institution = {Department of Chemistry, University of Southern California, Los Angeles,
	California 90089-1062, USA.},
  owner = {emilio},
  pmid = {20186976},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1002/prot.22687}
}

@ARTICLE{Singh2010a,
  author = {Nidhi Singh and Arieh Warshel},
  title = {A comprehensive examination of the contributions to the binding entropy
	of protein-ligand complexes.},
  journal = {Proteins},
  year = {2010},
  volume = {78},
  pages = {1724--1735},
  number = {7},
  month = {May},
  abstract = {One of the most important requirements in computer-aided drug design
	is the ability to reliably evaluate the binding free energies. However,
	the process of ligand binding is very complex because of the intricacy
	of the interrelated processes that are difficult to predict and quantify.
	In fact, the deeper understanding of the origin of the observed binding
	free energies requires the ability to decompose these free energies
	to their contributions from different interactions. Furthermore,
	it is important to evaluate the relative entropic and enthalpic contributions
	to the overall free energy. Such an evaluation is useful for assessing
	temperature effects and exploring specialized options in enzyme design.
	Unfortunately, calculations of binding entropies have been much more
	challenging than calculations of binding free energies. This work
	is probably the first to present microscopic evaluation of all of
	the relevant components to the binding entropy, namely configurational,
	polar solvation, and hydrophobic entropies. All of these contributions
	are evaluated by the restraint release approach. The calculated results
	shed an interesting light on major compensation effects in both the
	solvation and hydrophobic effect and, despite some overestimate,
	can provide very useful insight. This study also helps in analyzing
	some problems with the widely used molecular mechanics/Poisson-Boltzmann
	surface area approach.},
  doi = {10.1002/prot.22689},
  institution = {Department of Chemistry, University of Southern California, Los Angeles,
	California 90089-1062, USA.},
  owner = {emilio},
  pmid = {20186973},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1002/prot.22689}
}

@ARTICLE{Singh2009,
  author = {Nidhi Singh and Arieh Warshel},
  title = {Toward accurate microscopic calculation of solvation entropies: extending
	the restraint release approach to studies of solvation effects.},
  journal = {J Phys Chem B},
  year = {2009},
  volume = {113},
  pages = {7372--7382},
  number = {20},
  month = {May},
  abstract = {The evaluation of the solvation entropies is a major conceptual and
	practical challenge. On the one hand, it is interesting to quantify
	the factors that are responsible for the solvation entropies in solutions,
	whereas on the other, it is essential to be able to assess the contributions
	of the solvation entropies to the binding free energies and related
	properties. In fact, the solvation entropies are neglected in almost
	all of the studies of the binding entropies. The main problem is
	that widely used approaches, such as the quasiharmonic (QH) approximation,
	do not provide reliable results particularly in cases of shallow
	potential and multidimensional surfaces while brute force evaluations
	of the entropic effects by simulating temperature dependence of the
	free energy converges very slowly. This paper addresses the above
	issue by starting with an analysis of the factors that are responsible
	for the negative solvation entropy of ions, showing that it is not
	due to the change in the solvent vibration modes or to the solvent
	force constant but to the changes in the solvent configurational
	space upon change in the solute charges. We begin by clarifying that
	when one deals with aqueous solutions, it is easy to evaluate the
	corresponding entropic effect by the Langevin dipole (LD) treatment.
	However, in this work we are interested in developing a general microscopic
	tool that can be used to study similar effects in the proteins. To
	this end, we explore the ability of our restraint release (RR) approach
	to evaluate the solvation entropy. We start this analysis by reviewing
	the foundation of this approach and in particular, the requirements
	of minimizing the enthalpy contribution to the RR free energy. We
	then establish that our approach is not a specialized harmonic treatment
	but a rather powerful general approach. Moving to the main topic
	of this work, we demonstrate that the RR approach provides quantitative
	results for the solvation entropies of monovalent and divalent ions
	and effectively captures the physics of these entropic effects. The
	success of the current approach indicates that it should be applicable
	to the studies of the solvation entropies in the proteins and also,
	in examining hydrophobic effects. Thus, we believe that the RR approach
	provides a powerful tool for evaluating the corresponding contributions
	to the binding entropies and, eventually, to the binding free energies.
	This holds promise for extending the information theory modeling
	to proteins and protein-ligand complexes in aqueous solutions and
	consequently, facilitating computer-aided drug design.},
  doi = {10.1021/jp811063v},
  institution = {Department of Chemistry, 418 SGM Building, University of Southern
	California, 3620 McClintock Avenue, Los Angeles, California 90089-1062,
	USA.},
  keywords = {Entropy; Microscopy; Sensitivity and Specificity; Sodium; Solvents;
	Time Factors; Vibration},
  owner = {emilio},
  pmid = {19402609},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1021/jp811063v}
}

@ARTICLE{Singh:Mhaka:Christensen:Gray:Denmeade:Isaacs:2005,
  author = {Singh, P. and Mhaka, {A. M.} and Christensen, {S. B.} and Gray, {J.
	J.} and Denmeade, {S. R.} and Isaacs, {J. T.}},
  title = {Applying linear interaction energy method for rational drug design
	of noncompetitive allosteric inhibitors of the sarco- and endoplasmic
	reticulum Calcium-ATPase},
  journal = {J. Med. Chem.},
  year = {2005},
  volume = {48},
  pages = {3005--3014},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Sitkoff:Ben-Tai:Honig:96,
  author = {Sitkoff, D. and Ben-Tai, N. and Honig, B.},
  title = {Calculation of Alkane to Water Solvation Free Energies Using Continuum
	Solvent Models},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {2744-52},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Sitkoff:Sharp:Honig:94,
  author = {Sitkoff, D. and Sharp, K. A. and Honig, B.},
  title = {Correlating Solvation Free Energies and Surface Tensions of Hydrocarbon
	Solutes},
  journal = {Biophysical Chemistry},
  year = {1994},
  volume = {51},
  pages = {397-409},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Sitkoff:Sharp:Honig:94b,
  author = {Sitkoff, D. and Sharp, K. A. and Honig, B.},
  title = {Accurate calculation of hydration free energies using macroscopic
	solvent models},
  journal = {J. Phys. Chem.},
  year = {1994},
  volume = {98},
  pages = {1978-1988},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Skillman:2012,
  author = {Skillman, A.},
  title = {SAMPL3: blinded prediction of host-guest binding affinities, hydration
	free energies, and trypsin inhibitors},
  journal = {Journal of Computer-Aided Molecular Design},
  year = {2012},
  volume = {Online First},
  pages = {1--2},
  issn = {0920-654X},
  keywords = {Chemistry and Materials Science},
  owner = {emilio},
  publisher = {Springer Netherlands},
  timestamp = {2012.06.22},
  url = {http://dx.doi.org/10.1007/s10822-012-9580-z}
}

@ARTICLE{Skipper:93,
  author = {Skipper, N. T.},
  title = {Computer Simulation of Methane-Water Solutions. Evidence for a Temperature-Dependent
	Hydrophobic Attraction},
  journal = {Chem. Phys. Lett.},
  year = {1993},
  volume = {207},
  pages = {424},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Smith:Jorgensen:1998,
  author = {Smith Jr., {R. H.} and Jorgensen, {W. L.} and Tirado-Rives, J. and
	Lamb, {M. L.} and Janssen, {P. A. J.} and Michejda, {C. J.} and Kroeger
	Smith, {M. B.}},
  title = {Prediction of binding affinities for TIBO inhibitors of {HIV-1} reverse
	transcriptase using {M}onte {C}arlo simulations in a linear response
	method},
  journal = {J. Med. Chem.},
  year = {1998},
  volume = {41},
  pages = {5272--5286},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Smith:Haymet:93,
  author = {Smith, D. E. and Haymet, A. D. J.},
  title = {Free Energy, Entropy, and Internal Energy of Hydrophobic Interactions:
	Computer Simulations},
  journal = {J. Chem. Phys.},
  year = {1993},
  volume = {98},
  pages = {6445},
  number = {8},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Smith:Zhang:Haymet:92,
  author = {Smith, D. E. and Zhang, L. and Haymet, A. D. J.},
  title = {Entropy of Association of Methane in Water: A New Molecular Dynamics
	Computer Simulation},
  journal = {J. Am. Chem. Soc.},
  year = {1992},
  volume = {114},
  pages = {5876-5878},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Smith:93,
  author = {Smith, P. E. and Brunne, R. and Mark, A. E. and van Gunsteren, W.
	F.},
  journal = {J. Phys. Chem.},
  year = {1993},
  volume = {97},
  pages = {2009-2014},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Smith:vanGunsteren:94,
  author = {Smith, P. E. and van Gunsteren, W. F.},
  journal = {J. Chem. Phys.},
  year = {1994},
  volume = {100},
  pages = {577-585},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Smith:Arnold:Das:1995,
  author = {Smith, {M. B. K.} and Rouzer, {C. A.} and Taneyhill, {L. A.} and
	Smith, {N. A.} and Hughes, {S. H.} and Boyer, {P. L.} and Janssen,
	{P. A. J.} Moereels, H. and Koymans, L. and Arnold, E. and Ding,
	J. and Das, K. and Zhang, W. and Michejda, {C. J.} and Smith-Jr,
	{R. H.} },
  title = {Molecular modeling studies of {HIV-1} reverse transcriptase nonnucleoside
	inhibitors: Total energy of complexation as a predictor of drug placement
	and activity

	},
  journal = {Protein Sci.},
  year = {1995},
  volume = {4},
  pages = {2203--2222},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Snow:Nguyen:Pande:Gruebele:2002,
  author = {Snow, C. D. and Nguyen, H. and Pande, V. S. and Gruebele, M.},
  title = {Absolute comparison of simulated and experimental protein-folding
	dynamics},
  journal = {Nature},
  year = {2002},
  volume = {420},
  pages = {102-106},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Snow:Zagrovic:Pande:2002,
  author = {Snow, {C. D.} and Zagrovic, B. and Pande, {V. S.}},
  title = {The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular
	Dynamics Simulations},
  journal = {J. Am. Chem. Soc.},
  year = {2002},
  volume = {124},
  pages = {14548-14549},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Sousa2006,
  author = {Sérgio Filipe Sousa and Pedro Alexandrino Fernandes and Maria João
	Ramos},
  title = {Protein-ligand docking: current status and future challenges.},
  journal = {Proteins},
  year = {2006},
  volume = {65},
  pages = {15--26},
  number = {1},
  month = {Oct},
  abstract = {Understanding the ruling principles whereby protein receptors recognize,
	interact, and associate with molecular substrates and inhibitors
	is of paramount importance in drug discovery efforts. Protein-ligand
	docking aims to predict and rank the structure(s) arising from the
	association between a given ligand and a target protein of known
	3D structure. Despite the breathtaking advances in the field over
	the last decades and the widespread application of docking methods,
	several downsides still exist. In particular, protein flexibility-a
	critical aspect for a thorough understanding of the principles that
	guide ligand binding in proteins-is a major hurdle in current protein-ligand
	docking efforts that needs to be more efficiently accounted for.
	In this review the key concepts of protein-ligand docking methods
	are outlined, with major emphasis being given to the general strengths
	and weaknesses that presently characterize this methodology. Despite
	the size of the field, the principal types of search algorithms and
	scoring functions are reviewed and the most popular docking tools
	are briefly depicted. Recent advances that aim to address some of
	the traditional limitations associated with molecular docking are
	also described. A selection of hand-picked examples is used to illustrate
	these features.},
  doi = {10.1002/prot.21082},
  institution = {REQUIMTE, Departamento de Química, Faculdade de Ciências da Universidade
	do Porto, Porto, Portugal.},
  keywords = {Algorithms; Binding Sites; Computer Simulation; Ligands; Protein Binding;
	Protein Conformation; Proteins; Software; Water},
  owner = {emilio},
  pmid = {16862531},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1002/prot.21082}
}

@ARTICLE{Spolar:Livingstone:Record:92,
  author = {Spolar, R. S. and Livingstone, J. R. and Record, M. T. Jr.},
  title = {Use of Liquid Hydrocarbons and Amide Transfer Data To Estimate Contributions
	of Thermodynamic Functions of Protein Folding from the Removal of
	Nonpolar and Polar Surface from Water},
  journal = {Biochemistry},
  year = {1992},
  volume = {31},
  pages = {3947-3955},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Srinivasan:Cheatham:Cieplak:Kollman:Case:98,
  author = {Srinivasan, J. and {Cheatham III}, {T. E.} and Cieplak, P. and Kollman,
	{P. A.} and Case, {D. A.}},
  title = {Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA
	Helices},
  journal = {J. Am. Chem. Soc.},
  year = {1998},
  volume = {120},
  pages = {9401-9409},
  number = {37},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Srinivasan1998,
  author = {J. Srinivasan and J. Miller and P. A. Kollman and D. A. Case},
  title = {Continuum solvent studies of the stability of RNA hairpin loops and
	helices.},
  journal = {J Biomol Struct Dyn},
  year = {1998},
  volume = {16},
  pages = {671--682},
  number = {3},
  month = {Dec},
  abstract = {We apply continuum solvent models to investigate the relative stability
	of various conformational forms for two RNA sequences, GGAC(UUCG)GUCC
	and GGUG(UGAA)CACC. In the first part, we compare alternate hairpin
	conformations to explore the reliability of these models to discriminate
	between different local conformations. A second part looks at the
	hairpin-duplex conversion for the UUCG sequence, identifying major
	contributors to the thermodynamics of a much large scale transition.
	Structures were taken as snapshots from multi-nanosecond molecular
	dynamics simulations computed in a consistent fashion using explicit
	solvent and with long-range electrostatics accounted for using the
	Particle-Mesh Ewald procedure. The electrostatic contribution to
	solvation energies were computed using both a finite-difference Poisson-Boltzmann
	(PB) model and a pairwise Generalized Born model; non-electrostatic
	contributions were estimated with a surface-area dependent term.
	To these solvation free energies were added the mean solute internal
	energies (determined from a molecular mechanics potential) and estimates
	of the solute entropy (from a harmonic analysis). Consistent with
	experiment and with earlier solvated molecular dynamics simulations,
	the UUCG hairpin was found to prefer conformers close to a recent
	NMR structure determination in preference to those from an earlier
	NMR study. Similarly, results for the UGAA hairpin favored an NMR-derived
	structure over that to be expected for a generic GNRA hairpin loop.
	Experimental free energies are not known for the hairpin/duplex conversion,
	but must be close to zero since hairpins are seen in solution and
	duplexes in crystals; out calculations find a value near zero and
	illustrate the expected interplay of solvation, salt effects and
	entropy in affecting this equilibrium.},
  institution = {Department of Molecular Biology, The Scripps Research Institute,
	La Jolla, CA 92037, USA.},
  keywords = {Computer Simulation; Dose-Response Relationship, Drug; Models, Molecular;
	Models, Statistical; Molecular Conformation; RNA; Salts; Solvents;
	Static Electricity},
  owner = {emilio},
  pmid = {10052623},
  timestamp = {2010.04.21}
}

@ARTICLE{Steinbrecher2011,
  author = {Steinbrecher, Thomas and Joung, InSuk and Case, David A.},
  title = {Soft-core potentials in thermodynamic integration: Comparing one-
	and two-step transformations},
  journal = {J. Comput. Chem.},
  year = {2011},
  volume = {32},
  pages = {3253--3263},
  number = {15},
  abstract = {Molecular dynamics-based free energy calculations allow the determination
	of a variety of thermodynamic quantities from computer simulations
	of small molecules. Thermodynamic integration (TI) calculations can
	suffer from instabilities during the creation or annihilation of
	particles. This “singularity” problem can be addressed with “soft-core”
	potential functions which keep pairwise interaction energies finite
	for all configurations and provide smooth free energy curves. “One-step”
	transformations, in which electrostatic and van der Waals forces
	are simultaneously modified, can be simpler and less expensive than
	“two-step” transformations in which these properties are changed
	in separate calculations. Here, we study solvation free energies
	for molecules of different hydrophobicity using both models. We provide
	recommended values for the two parameters αLJ and βC controlling
	the behavior of the soft-core Lennard–Jones and Coulomb potentials
	and compare one- and two-step transformations with regard to their
	suitability for numerical integration. For many types of transformations,
	the one-step procedure offers a convenient and accurate approach
	to free energy estimates. © 2011 Wiley Periodicals, Inc. J Comput
	Chem, 2011},
  issn = {1096-987X},
  keywords = {free energy calculation, molecular dynamics, thermodynamic integration,
	free energy of salvation, numerical algorithms, separation shifted
	scaling, soft-core potentials},
  owner = {emilio},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  timestamp = {2011.11.06},
  url = {http://dx.doi.org/10.1002/jcc.21909}
}

@ARTICLE{Steinbrecher2007,
  author = {Thomas Steinbrecher and David L Mobley and David A Case},
  title = {Nonlinear scaling schemes for Lennard-Jones interactions in free
	energy calculations.},
  journal = {J Chem Phys},
  year = {2007},
  volume = {127},
  pages = {214108},
  number = {21},
  month = {Dec},
  abstract = {Alchemical free energy calculations provide a means for the accurate
	determination of free energies from atomistic simulations and are
	increasingly used as a tool for computational studies of protein-ligand
	interactions. Much attention has been placed on efficient ways to
	deal with the "endpoint singularity" effect that can cause simulation
	instabilities when changing the number of atoms. In this study we
	compare the performance of linear and several nonlinear transformation
	methods, among them separation shifted "soft core" scaling, for a
	popular test system, the hydration free energy of an amino acid side
	chain. All the nonlinear methods yield similar results if extensive
	sampling is performed, but soft core scaling provides smooth lambda
	curves that are best suited for commonly used numerical integration
	schemes. Additionally, results from a more flexible solute, hexane,
	will also be discussed.},
  doi = {10.1063/1.2799191},
  institution = {Department of Molecular Biology, The Scripps Research Institute,
	La Jolla, San Diego, California 92037, USA. steinbrt@scripps.edu},
  keywords = {Amino Acids; Computer Simulation; Energy Transfer; Ligands; Protein
	Binding; Solvents; Thermodynamics},
  owner = {emilio},
  pmid = {18067350},
  timestamp = {2011.01.31},
  url = {http://dx.doi.org/10.1063/1.2799191}
}

@ARTICLE{Stern2007,
  author = {Harry A Stern},
  title = {Molecular simulation with variable protonation states at constant
	pH.},
  journal = {J Chem Phys},
  year = {2007},
  volume = {126},
  pages = {164112},
  number = {16},
  month = {Apr},
  abstract = {A new method is presented for performing molecular simulations at
	constant pH. The method is a Monte Carlo procedure where trial moves
	consist of relatively short molecular dynamics trajectories, using
	a time-dependent potential energy that interpolates between the old
	and new protonation states. Conformations and protonation states
	are sampled from the correct statistical ensemble independent of
	the trial-move trajectory length, which may be adjusted to optimize
	efficiency. Because moves are not instantaneous, the method does
	not require the use of a continuum solvation model. It should also
	be useful in describing buried titratable groups that are not directly
	exposed to solvent, but have strong interactions with neighboring
	hydrogen bond partners. The feasibility of the method is demonstrated
	for a simple test case: constant-pH simulations of acetic acid in
	aqueous solution with an explicit representation of water molecules.},
  doi = {10.1063/1.2731781},
  institution = {Department of Chemistry, University of Rochester, Rochester, New
	York 14627, USA.},
  owner = {emilio},
  pmid = {17477594},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1063/1.2731781}
}

@ARTICLE{Still:90,
  author = {Still, W. C. Tempczyk, A. and Hawley, R. C. and Hendrikson, T.},
  title = {Semianalytical treatment of solvation for molecular mechanics and
	dynamics},
  journal = {J. Am. Chem. Soc.},
  year = {1990},
  volume = {112},
  pages = {6127-6129},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Stillinger:Rahman:74,
  author = {Stillinger, F. and Rahman, A.},
  journal = {J. Chem. Phys.},
  year = {1974},
  volume = {60},
  pages = {1545-1552},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Stillinger:73,
  author = {Stillinger, F. H.},
  title = {Structure in Aqueous Solutions of Nonpolar Solutes from the Standpoint
	of Scaled-Particle Theory},
  journal = {J. of Solution Chemistry},
  year = {1973},
  volume = {2},
  pages = {141-158},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Straatsma:Berendsen:Postma:86,
  author = {Straatsma, T. P. and Berendsen, J. C. and Postma, J. P. N.},
  title = {Free Energy of Hydrophobic Hydration: A Molecular Dynamics Study
	of Noble Gases in Water},
  journal = {J. Chem. Phys.},
  year = {1986},
  volume = {85},
  pages = {6720},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Sturtevant:77,
  author = {Sturtevant, J. M.},
  title = {Heat Capacity and Entropy Changes in Processes Involving Proteins},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1977},
  volume = {74},
  pages = {2236-2240},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Su:Gallicchio:Levy:2004,
  author = {Su, Y. and Gallicchio, E.},
  title = {The non-polar solvent potential of mean force for the dimerization
	of alanine dipeptide: The role of solute-solvent van der Waals interactions},
  journal = {Biophys. Chem.},
  year = {2004},
  volume = {109},
  pages = {251--260},
  owner = {emilio},
  timestamp = {2010.10.28}
}

@ARTICLE{Su:Gallicchio:Levy:2007,
  author = {Su, Y. and Gallicchio, E. and Das, K. and Arnold, E. and Levy, {R.
	M.}},
  title = {Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit
	Solvent: Theory and Application to the Binding of NNRTIs to HIV-1
	Reverse Transcriptase},
  journal = {J. Chem. Theory Comput.},
  year = {2007},
  volume = {3},
  pages = {256--277},
  owner = {emilio},
  timestamp = {2010.10.28}
}

@ARTICLE{Sugita2000,
  author = {Yuji Sugita and Akio Kitao and Yuko Okamoto},
  title = {Multidimensional replica-exchange method for free-energy calculations},
  journal = {The Journal of Chemical Physics},
  year = {2000},
  volume = {113},
  pages = {6042-6051},
  number = {15},
  doi = {10.1063/1.1308516},
  keywords = {free energy; digital simulation},
  owner = {emilio},
  publisher = {AIP},
  timestamp = {2011.01.18},
  url = {http://link.aip.org/link/?JCP/113/6042/1}
}

@ARTICLE{Sugita:Okamoto:1999,
  author = {Sugita, Y. and Okamoto, Y.},
  title = {Replica-exchange Molecular Dynamics Method for Protein Folding},
  journal = {Chem. Phys. Lett.},
  year = {1999},
  volume = {314},
  pages = {141--151},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Sulea2003,
  author = {Traian Sulea and Enrico O Purisima},
  title = {Profiling charge complementarity and selectivity for binding at the
	protein surface.},
  journal = {Biophys J},
  year = {2003},
  volume = {84},
  pages = {2883--2896},
  number = {5},
  month = {May},
  abstract = {A novel analysis and representation of the protein surface in terms
	of electrostatic binding complementarity and selectivity is presented.
	The charge optimization methodology is applied in a probe-based approach
	that simulates the binding process to the target protein. The molecular
	surface is color coded according to calculated optimal charge or
	according to charge selectivity, i.e., the binding cost of deviating
	from the optimal charge. The optimal charge profile depends on both
	the protein shape and charge distribution whereas the charge selectivity
	profile depends only on protein shape. High selectivity is concentrated
	in well-shaped concave pockets, whereas solvent-exposed convex regions
	are not charge selective. This suggests the synergy of charge and
	shape selectivity hot spots toward molecular selection and recognition,
	as well as the asymmetry of charge selectivity at the binding interface
	of biomolecular systems. The charge complementarity and selectivity
	profiles map relevant electrostatic properties in a readily interpretable
	way and encode information that is quite different from that visualized
	in the standard electrostatic potential map of unbound proteins.},
  doi = {10.1016/S0006-3495(03)70016-2},
  institution = {Biotechnology Research Institute, National Research Council of Canada,
	Montreal, Quebec H4P 2R2, Canada.},
  keywords = {Binding Sites; Color; Computer Simulation; Electrochemistry; Energy
	Transfer; Macromolecular Substances; Models, Molecular; Nerve Tissue
	Proteins; Protein Binding; Protein Structure, Tertiary; Proteins;
	Reproducibility of Results; Sensitivity and Specificity; Static Electricity;
	Surface Properties; Trypsin; User-Computer Interface},
  owner = {emilio},
  pii = {S0006-3495(03)70016-2},
  pmid = {12719221},
  timestamp = {2010.05.20},
  url = {http://dx.doi.org/10.1016/S0006-3495(03)70016-2}
}

@ARTICLE{Sulea2009,
  author = {Traian Sulea and Duangporn Wanapun and Sheldon Dennis and Enrico
	O Purisima},
  title = {Prediction of SAMPL-1 hydration free energies using a continuum electrostatics-dispersion
	model.},
  journal = {J Phys Chem B},
  year = {2009},
  volume = {113},
  pages = {4511--4520},
  number = {14},
  month = {Apr},
  abstract = {The SAMPL-1 hydration free energy blind prediction challenge data
	set includes 63 compounds that are more chemically diverse, polyfunctional,
	drug-like, and with examples of transfer free energies and molecular
	weights larger than ever before seen in previously tabulated data
	sets of neutral compounds. For the prospective SAMPL-1 study, we
	employed a continuum model including a boundary element solution
	of the Poisson equation to describe electrostatic solvation, a molecular
	surface area-based cost of cavity formation in water, and a continuum
	Lennard-Jones potential to account for dispersion-repulsion solute-solvent
	effects. For the latter contribution, continuum van der Waals atom-type
	coefficients were calibrated and validated on previously available
	hydration data sets. In the prospective study, this continuum hydration
	model yielded SAMPL-1 predictions highly correlated with experimental
	data, albeit with a slope of slightly above 0.5, suggesting a valid
	model but with a systematic error. Analysis of the major outliers,
	all overestimating the experimental hydration data, highlights a
	common structural theme as a possible cause of the prediction errors:
	densely polar and hydrogen-bond-capable structures, featuring primarily
	substituted (sulfon)amide groups, often in conjugated systems. By
	examining analog pairs within the SAMPL-1 data set, it was also noted
	that certain solvation trends are captured neither by chemical sense
	nor by our hydration model, which seem too additive. A retrospective
	analysis of model transferability between hydration data sets as
	a function of its parameters and complexity indicates that the electrostatic
	component of the model is fairly transferrable across data sets,
	but the nonelectrostatic terms are less so. For the chemical space
	covered in SAMPL-1, absolute prediction errors indicate that the
	simpler transferrable electrostatics-only model outperforms the more
	complex model including cavity and continuum dispersion terms. Possible
	directions to further improve this continuum hydration model are
	proposed.},
  doi = {10.1021/jp8061477},
  institution = {Biotechnology Research Institute, National Research Council Canada,
	6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada.},
  keywords = {Amides; Databases, Factual; Models, Chemical; Reproducibility of Results;
	Static Electricity; Sulfhydryl Compounds; Thermodynamics; Urea; Water},
  owner = {emilio},
  pmid = {19267492},
  timestamp = {2010.05.20},
  url = {http://dx.doi.org/10.1021/jp8061477}
}

@ARTICLE{Sun:Kollman:92,
  author = {Sun, Y. and Spellmeyer, D. and Pearlman, D. A. and Kollman, P.},
  title = {Simulation of the Solvation Free Energies for Methane, Ethane, and
	Propane and Corresponding Amino Acid Dipeptides: A Critical Test
	of the Bond-PMF Correction, a new set of Hydrocarbon Parameters,
	and the Gas Phase-Water Hydrophobicity Scale},
  journal = {J. Am. Chem. Soc.},
  year = {1992},
  volume = {114},
  pages = {6798},
  number = {17},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Swanson2004,
  author = {Jessica M J Swanson and Richard H Henchman and J. Andrew McCammon},
  title = {Revisiting free energy calculations: a theoretical connection to
	MM/PBSA and direct calculation of the association free energy.},
  journal = {Biophys J},
  year = {2004},
  volume = {86},
  pages = {67--74},
  number = {1 Pt 1},
  month = {Jan},
  abstract = {The prediction of absolute ligand-receptor binding affinities is essential
	in a wide range of biophysical queries, from the study of protein-protein
	interactions to structure-based drug design. End-point free energy
	methods, such as the Molecular Mechanics Poisson-Boltzmann Surface
	Area (MM/PBSA) model, have received much attention and widespread
	application in recent literature. These methods benefit from computational
	efficiency as only the initial and final states of the system are
	evaluated, yet there remains a need for strengthening their theoretical
	foundation. Here a clear connection between statistical thermodynamics
	and end-point free energy models is presented. The importance of
	the association free energy, arising from one molecule's loss of
	translational and rotational freedom from the standard state concentration,
	is addressed. A novel method for calculating this quantity directly
	from a molecular dynamics simulation is described. The challenges
	of accounting for changes in the protein conformation and its fluctuations
	from separate simulations are discussed. A simple first-order approximation
	of the configuration integral is presented to lay the groundwork
	for future efforts. This model has been applied to FKBP12, a small
	immunophilin that has been widely studied in the drug industry for
	its potential immunosuppressive and neuroregenerative effects.},
  doi = {10.1016/S0006-3495(04)74084-9},
  institution = {Howard Hughes Medical Institute, Center for Theoretical Biological
	Physics, Department of Chemistry and Biochemistry, La Jolla, California.
	jswanson@mccammon.ucsd.edu},
  keywords = {Binding Sites; Computer Simulation; Energy Transfer; Kinetics; Models,
	Chemical; Models, Molecular; Protein Binding; Protein Conformation;
	Tacrolimus Binding Protein 1A, chemistry},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {S0006-3495(04)74084-9},
  pmid = {14695250},
  timestamp = {2011.02.03},
  url = {http://dx.doi.org/10.1016/S0006-3495(04)74084-9}
}

@ARTICLE{Swanson2005,
  author = {Jessica M J Swanson and John Mongan and J. Andrew McCammon},
  title = {Limitations of atom-centered dielectric functions in implicit solvent
	models.},
  journal = {J Phys Chem B},
  year = {2005},
  volume = {109},
  pages = {14769--14772},
  number = {31},
  month = {Aug},
  abstract = {Many recent advances in Poisson-Boltzmann and generalized Born implicit
	solvent models have used atom-centered polynomial or Gaussian functions
	to define the boundary separating low and high dielectric regions.
	In contrast to the Lee and Richards molecular surface, atom-centered
	surfaces result in interatomic crevices and buried pockets of high
	dielectric which are too small for a solvent molecule to occupy.
	We show that these interstitial high dielectric regions are of significant
	magnitude in globular proteins, that they artificially increase solvation
	energies, and that they distort the free energy surface of nonbonded
	interactions. These results suggest that implicit solvent dielectric
	functions must exclude interstitial high dielectric regions in order
	to yield physically meaningful results.},
  doi = {10.1021/jp052883s},
  keywords = {Electrons; Histidine, chemistry; Models, Chemical; Solutions; Solvents,
	chemistry; Static Electricity},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {16852866},
  timestamp = {2011.02.03},
  url = {http://dx.doi.org/10.1021/jp052883s}
}

@ARTICLE{Swanson:Mongan:McCammon:2005,
  author = {Swanson, Jessica M. J. and Mongan, John and McCammon, J. Andrew},
  title = {Limitations of Atom-Centered Dielectric Functions in Implicit Solvent
	Models},
  journal = {J. Phys. Chem. B},
  year = {2005},
  volume = {109},
  pages = {14769--14772},
  number = {31},
  doi = {10.1021/jp052883s},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp052883s},
  owner = {emilio},
  timestamp = {2011.01.18},
  url = {http://pubs.acs.org/doi/abs/10.1021/jp052883s}
}

@ARTICLE{Swendsen:Wang:1986,
  author = {Swendsen, {R. H.} and Wang, J.-S. },
  title = {Replica Monte Carlo Simulation of Spin-Glasses},
  journal = {Phys. Rev. Lett.},
  year = {1986},
  volume = {57},
  pages = {2607--2609},
  number = {21},
  month = {Nov},
  doi = {10.1103/PhysRevLett.57.2607},
  numpages = {2},
  owner = {emilio},
  publisher = {American Physical Society},
  timestamp = {2011.01.18}
}

@ARTICLE{Tan2004,
  author = {Tan, Zhiqiang},
  title = {On a Likelihood Approach for Monte Carlo Integration},
  journal = {J. Am. Stat. Assoc.},
  year = {2004},
  volume = {99},
  pages = {1027-1036},
  number = {468},
  abstract = { The use of estimating equations has been a common approach for constructing
	Monte Carlo estimators. Recently, Kong et al. proposed a formulation
	of Monte Carlo integration as a statistical model, making explicit
	what information is ignored and what is retained about the baseline
	measure. From simulated data, the baseline measure is estimated by
	maximum likelihood, and then integrals of interest are estimated
	by substituting the estimated measure. For two different situations
	in which independent observations are simulated from multiple distributions,
	we show that this likelihood approach achieves the lowest asymptotic
	variance possible by using estimating equations. In the first situation,
	the normalizing constants of the design distributions are estimated,
	and Meng and Wong's bridge sampling estimating equation is considered.
	In the second situation, the values of the normalizing constants
	are known, thereby imposing linear constraints on the baseline measure.
	Estimating equations including Hesterberg's stratified importance
	sampling estimator, Veach and Guibas's multiple importance sampling
	estimator, and Owen and Zhou's method of control variates are considered.
	},
  doi = {10.1198/016214504000001664},
  eprint = {http://pubs.amstat.org/doi/pdf/10.1198/016214504000001664},
  url = {http://pubs.amstat.org/doi/abs/10.1198/016214504000001664}
}

@ARTICLE{Tan2012,
  author = {Tan, Zhiqiang and Gallicchio, Emilio and Lapelosa, Mauro and Levy,
	Ronald M.},
  title = {Theory of binless multi-state free energy estimation with applications
	to protein-ligand binding},
  journal = {The Journal of Chemical Physics},
  year = {2012},
  volume = {136},
  pages = {144102},
  number = {14},
  keywords = {proteins},
  owner = {emilio},
  publisher = {AIP},
  timestamp = {2012.06.21},
  url = {http://dx.doi.org/10.1063/1.3701175}
}

@ARTICLE{Tanaka:Nakanishi:91,
  author = {Tanaka, H. and Nakanishi, K.},
  title = {Hydrophobic Hydration of Inert Gases; Thermodynamic Properties, Inherent
	Structures, and Normal-Mode Analysis},
  journal = {J. Chem. Phys.},
  year = {1991},
  volume = {95},
  pages = {3719},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Tanford:73,
  title = {The hydrophobic effect: formation of micelles and biological membranes},
  publisher = {Wiley},
  year = {1973},
  author = {Tanford, C.},
  address = {New York},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tanford:Kirkwood:57,
  author = {Tanford, C. and Kirkwood, J. G.},
  journal = {J. Am. Chem. Soc.},
  year = {1957},
  volume = {79},
  pages = {5333-5337},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tanford:79,
  author = {Tanford,C. H.},
  journal = {Proc. Natl. Acad. Sci.},
  year = {1979},
  volume = {76},
  pages = {4175-4176},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{McCammon:84,
  author = {Tembe, B. L. and McCammon, J. A.},
  title = {Ligand-Receptor Interactions},
  journal = {Comput. Chem.},
  year = {1984},
  volume = {8},
  pages = {281},
  number = {4},
  owner = {emilio},
  timestamp = {2010.11.01}
}

@ARTICLE{Terry:2004,
  author = {Terry, P. and Shan, A. and Huttunen, P.},
  title = {Improving Application Performance on HPC Systems with Process Synchronization},
  journal = {Linux Journal},
  year = {2004},
  volume = {127},
  pages = {68--73},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tjong:Zhou:2007a,
  author = {Tjong, H. and Zhou, {H.-X.}},
  title = {GBr6: A Parameterization-Free, Accurate, Analytical Generalized Born
	Method},
  journal = {J. Phys. Chem. B},
  year = {2007},
  volume = {111},
  pages = {3055--3061},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tjong:Zhou:2007b,
  author = {Tjong, H. and Zhou, {H.-X.}},
  title = {GBr6NL: A generalized Born method for accurately reproducing solvation
	energy of the nonlinear Poisson-Boltzmann equation},
  journal = {J. Chem. Phys.},
  year = {2007},
  volume = {126},
  pages = {195102},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tobias:Brooks:90,
  author = {Tobias, D. J. and Brooks, C. L.},
  title = {The Thermodynamics of Solvophobic Effects: A Molecular Dynamics Study
	of $n$-Butane in Carbon Tetrachloride and Water},
  journal = {J. Chem. Phys.},
  year = {1990},
  volume = {92},
  pages = {2582},
  number = {4},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tomasi:Persico:94,
  author = {Tomasi, J. and Persico, M.},
  title = {Molecular Interactions in Solution: An Overview of Methods Based
	on Continuous Distributions of the Solvent},
  journal = {Chem. Rev.},
  year = {1994},
  volume = {94},
  pages = {2027-2094},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tounge:Reynolds:2003,
  author = {Tounge, {B. A.} and Reynolds, {C. H.}},
  title = {Calculation of the Binding Affinity of $\beta$-Secretase Inhibitors
	Using the Linear Interaction Energy Method},
  journal = {J. Med. Chem.},
  year = {2003},
  volume = {46},
  pages = {2074--2082},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Schulten:92,
  author = {Treutlein, H. and Schulten, K. and Br{\"{u}}nger, A. T. and Karplus,
	M. and Deisenhofer, J. and Michel, H.},
  title = {Chromophore-protein interactions and the function of the photosynthetic
	reaction center: A molecular dynamics study},
  journal = {Proc. Natl. Acad. Sci.. USA},
  year = {1992},
  volume = {89},
  pages = {75-79},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Trott2010,
  author = {Oleg Trott and Arthur J Olson},
  title = {AutoDock Vina: improving the speed and accuracy of docking with a
	new scoring function, efficient optimization, and multithreading.},
  journal = {J. Comput. Chem.},
  year = {2010},
  volume = {31},
  pages = {455--461},
  number = {2},
  month = {Jan},
  abstract = {AutoDock Vina, a new program for molecular docking and virtual screening,
	is presented. AutoDock Vina achieves an approximately two orders
	of magnitude speed-up compared with the molecular docking software
	previously developed in our lab (AutoDock 4), while also significantly
	improving the accuracy of the binding mode predictions, judging by
	our tests on the training set used in AutoDock 4 development. Further
	speed-up is achieved from parallelism, by using multithreading on
	multicore machines. AutoDock Vina automatically calculates the grid
	maps and clusters the results in a way transparent to the user.},
  doi = {10.1002/jcc.21334},
  institution = {Department of Molecular Biology, The Scripps Research Institute,
	La Jolla, California, USA.},
  keywords = {Algorithms; Automation; Binding Sites; Computational Biology, methods;
	Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Ligands;
	Molecular Dynamics Simulation; Sensitivity and Specificity; Software;
	Solvents, chemistry; Thermodynamics; Time Factors},
  language = {eng},
  medline-pst = {ppublish},
  owner = {mauro},
  pmid = {19499576},
  timestamp = {2011.09.19},
  url = {http://dx.doi.org/10.1002/jcc.21334}
}

@ARTICLE{Truskett:Debenedetti:2001,
  author = {Truskett, T. M. and Debenedetti, P. G. and Torquato, S.},
  title = {Thermodynamic implications of confinement for a waterlike fluid},
  journal = {J. Chem. Phys.},
  year = {2001},
  volume = {114},
  pages = {2401},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tsui:Case:2000,
  author = {Tsui, V. and Case, D. A.},
  title = {Theory and applications of the generalized Born solvation model in
	macromolecular simulations},
  journal = {Biopolymers},
  year = {2000},
  volume = {56},
  pages = {275-291},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tsui:Case:2000a,
  author = {Tsui, V. and Case, D. A.},
  title = {Molecular Dynamics Simulations of Nucleic Acids with a Generalized
	Born Solvation Model},
  journal = {J. Am. Chem. Soc.},
  year = {2000},
  volume = {122},
  pages = {2489-2498},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tunon:Silla:Pascual:93,
  author = {Tu\~{n}\'{o}n, I. and Silla, E. and Pascual-Ahuir, J. L.},
  journal = {Chem. Phys. Lett.},
  year = {1993},
  volume = {203},
  pages = {289},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Tuckerman:92,
  author = {Tuckerman, A. M. and Berne, B. J. and Martyna, G. J.},
  journal = {J. Chem. Phys.},
  year = {1992},
  volume = {97},
  pages = {1990-1998},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Turjanski2008,
  author = {Adrian Gustavo Turjanski and J. Silvio Gutkind and Robert B Best
	and Gerhard Hummer},
  title = {Binding-induced folding of a natively unstructured transcription
	factor.},
  journal = {PLoS Comput Biol},
  year = {2008},
  volume = {4},
  pages = {e1000060},
  number = {4},
  month = {Apr},
  abstract = {Transcription factors are central components of the intracellular
	regulatory networks that control gene expression. An increasingly
	recognized phenomenon among human transcription factors is the formation
	of structure upon target binding. Here, we study the folding and
	binding of the pKID domain of CREB to the KIX domain of the co-activator
	CBP. Our simulations of a topology-based Gō-type model predict a
	coupled folding and binding mechanism, and the existence of partially
	bound intermediates. From transition-path and Phi-value analyses,
	we find that the binding transition state resembles the unstructured
	state in solution, implying that CREB becomes structured only after
	committing to binding. A change of structure following binding is
	reminiscent of an induced-fit mechanism and contrasts with models
	in which binding occurs to pre-structured conformations that exist
	in the unbound state at equilibrium. Interestingly, increasing the
	amount of structure in the unbound pKID reduces the rate of binding,
	suggesting a "fly-casting"-like process. We find that the inclusion
	of attractive non-native interactions results in the formation of
	non-specific encounter complexes that enhance the on-rate of binding,
	but do not significantly change the binding mechanism. Our study
	helps explain how being unstructured can confer an advantage in protein
	target recognition. The simulations are in general agreement with
	the results of a recently reported nuclear magnetic resonance study,
	and aid in the interpretation of the experimental binding kinetics.},
  doi = {10.1371/journal.pcbi.1000060},
  institution = {Oral and Pharyngeal Cancer Branch, National Institute of Dental and
	Craniofacial Research, National Institutes of Health, Bethesda, Maryland,
	United States of America.},
  keywords = {Amino Acid Sequence; Binding Sites; CREB-Binding Protein, chemistry/ultrastructure;
	Computer Simulation; Humans; Models, Chemical; Models, Molecular;
	Molecular Sequence Data; Protein Binding; Protein Conformation; Protein
	Folding; Protein Structure, Tertiary; Sequence Analysis, Protein,
	methods; Transcription Factors, chemistry/ultrastructure},
  language = {eng},
  medline-pst = {epublish},
  owner = {emilio},
  pmid = {18404207},
  timestamp = {2011.07.15},
  url = {http://dx.doi.org/10.1371/journal.pcbi.1000060}
}

@ARTICLE{Turner1999,
  author = {B. G. Turner and M. F. Summers},
  title = {Structural biology of HIV.},
  journal = {J Mol Biol},
  year = {1999},
  volume = {285},
  pages = {1--32},
  number = {1},
  month = {Jan},
  abstract = {The human immunodeficiency virus (HIV) genome encodes a total of three
	structural proteins, two envelope proteins, three enzymes, and six
	accessory proteins. Studies over the past ten years have provided
	high-resolution three-dimensional structural information for all
	of the viral enzymes, structural proteins and envelope proteins,
	as well as for three of the accessory proteins. In some cases it
	has been possible to solve the structures of the intact, native proteins,
	but in most cases structural data were obtained for isolated protein
	domains, peptidic fragments, or mutants. Peptide complexes with two
	regulatory RNA fragments and a protein complex with an RNA recognition/encapsidation
	element have also been structurally characterized. This article summarizes
	the high-resolution structural information that is currently available
	for HIV proteins and reviews current structure-function and structure-biological
	relationships.},
  doi = {10.1006/jmbi.1998.2354},
  institution = {Howard Hughes Medical Institute, Department of Chemistry, University
	of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD,
	21250, USA.},
  keywords = {Animals; HIV; HIV Envelope Protein gp120; HIV Envelope Protein gp41;
	Humans; Protein Conformation; Viral Proteins; Viral Structural Proteins;
	Virion; Virus Replication},
  owner = {emilio},
  pii = {S0022-2836(98)92354-3},
  pmid = {9878383},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1006/jmbi.1998.2354}
}

@ARTICLE{Vanden-Eijnden2008,
  author = {Eric Vanden-Eijnden and Maddalena Venturoli and Giovanni Ciccotti
	and Ron Elber},
  title = {On the assumptions underlying milestoning.},
  journal = {J Chem Phys},
  year = {2008},
  volume = {129},
  pages = {174102},
  number = {17},
  month = {Nov},
  abstract = {Milestoning is a procedure to compute the time evolution of complicated
	processes such as barrier crossing events or long diffusive transitions
	between predefined states. Milestoning reduces the dynamics to transition
	events between intermediates (the milestones) and computes the local
	kinetic information to describe these transitions via short molecular
	dynamics (MD) runs between the milestones. The procedure relies on
	the ability to reinitialize MD trajectories on the milestones to
	get the right kinetic information about the transitions. It also
	rests on the assumptions that the transition events between successive
	milestones and the time lags between these transitions are statistically
	independent. In this paper, we analyze the validity of these assumptions.
	We show that sets of optimal milestones exist, i.e., sets such that
	successive transitions are indeed statistically independent. The
	proof of this claim relies on the results of transition path theory
	and uses the isocommittor surfaces of the reaction as milestones.
	For systems in the overdamped limit, we also obtain the probability
	distribution to reinitialize the MD trajectories on the milestones,
	and we discuss why this distribution is not available in closed form
	for systems with inertia. We explain why the time lags between transitions
	are not statistically independent even for optimal milestones, but
	we show that working with such milestones allows one to compute mean
	first passage times between milestones exactly. Finally, we discuss
	some practical implications of our results and we compare milestoning
	with Markov state models in view of our findings.},
  doi = {10.1063/1.2996509},
  institution = {Courant Institute of Mathematical Sciences, New York University,
	New York, New York 10012, USA. eve2@cims.nyu.edu},
  keywords = {Kinetics; Models, Chemical; Reproducibility of Results; Surface Properties;
	Time Factors},
  owner = {emilio},
  pmid = {19045328},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1063/1.2996509}
}

@ARTICLE{Varadarajan:Sturtevant:92,
  author = {Varadarajan, R. and Connelly, P. R. and Sturtevant, J. M. and Richards,
	F. M.},
  title = {Heat Capacity Changes for Protein-Peptide Interactions in the Ribonuclease
	{S} System},
  journal = {Biochemistry},
  year = {1992},
  volume = {31},
  pages = {1421-1426},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Vitalis:Pappu:2008,
  author = {Vitalis, A. and Pappu, {R. V.}},
  title = {{ABSINTH}: A new continuum solvation model for simulations of polypeptides
	in aqueous solutions},
  journal = {J. Comp. Chem.},
  year = {2009},
  volume = {30},
  pages = {673-699},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Voelz2010,
  author = {Vincent A Voelz and Gregory R Bowman and Kyle Beauchamp and Vijay
	S Pande},
  title = {Molecular simulation of ab initio protein folding for a millisecond
	folder NTL9(1-39).},
  journal = {J Am Chem Soc},
  year = {2010},
  volume = {132},
  pages = {1526--1528},
  number = {5},
  month = {Feb},
  abstract = {To date, the slowest-folding proteins folded ab initio by all-atom
	molecular dynamics simulations have had folding times in the range
	of nanoseconds to microseconds. We report simulations of several
	folding trajectories of NTL9(1-39), a protein which has a folding
	time of approximately 1.5 ms. Distributed molecular dynamics simulations
	in implicit solvent on GPU processors were used to generate ensembles
	of trajectories out to approximately 40 micros for several temperatures
	and starting states. At a temperature less than the melting point
	of the force field, we observe a small number of productive folding
	events, consistent with predictions from a model of parallel uncoupled
	two-state simulations. The posterior distribution of the folding
	rate predicted from the data agrees well with the experimental folding
	rate (approximately 640/s). Markov State Models (MSMs) built from
	the data show a gap in the implied time scales indicative of two-state
	folding and heterogeneous pathways connecting diffuse mesoscopic
	substates. Structural analysis of the 14 out of 2000 macrostates
	transited by the top 10 folding pathways reveals that native-like
	pairing between strands 1 and 2 only occurs for macrostates with
	p(fold) > 0.5, suggesting beta(12) hairpin formation may be rate-limiting.
	We believe that using simulation data such as these to seed adaptive
	resampling simulations will be a promising new method for achieving
	statistically converged descriptions of folding landscapes at longer
	time scales than ever before.},
  doi = {10.1021/ja9090353},
  institution = {Department of Chemistry, Stanford University, Stanford, California
	94305, USA.},
  keywords = {Arabidopsis; Markov Chains; Molecular Dynamics Simulation; Protein
	Conformation; Protein Folding; Time Factors; Transcription Factors},
  owner = {emilio},
  pmid = {20070076},
  timestamp = {2010.11.03},
  url = {http://dx.doi.org/10.1021/ja9090353}
}

@ARTICLE{Vorobyov:Li:Allen:2008,
  author = {Vorobyov, I. and Li, L. and and Allen, {T. W.}},
  title = {Assessing Atomistic and Coarse-Grained Force Fields for Protein--Lipid
	Interactions: the Formidable Challenge of an Ionizable Side Chain
	in a Membrane},
  journal = {J. Phys. Chem. B},
  year = {2008},
  volume = {112},
  pages = {9588--9602},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wade2005,
  author = {Rebecca C Wade and Domantas Motiejunas and Karin Schleinkofer and
	Sudarko and Peter J Winn and Amit Banerjee and Andrei Kariakin and
	Christiane Jung},
  title = {Multiple molecular recognition mechanisms. Cytochrome P450--a case
	study.},
  journal = {Biochim Biophys Acta},
  year = {2005},
  volume = {1754},
  pages = {239--244},
  number = {1-2},
  month = {Dec},
  abstract = {Biomolecular recognition is complex. The balance between the different
	molecular properties that contribute to molecular recognition, such
	as shape, electrostatics, dynamics and entropy, varies from case
	to case. This, along with the extent of experimental characterization,
	influences the choice of appropriate computational approaches to
	study biomolecular interactions. Here, we present computational studies
	of cytochrome P450 enzymes and their interactions with small molecules
	and with other proteins. These interactions exemplify some of the
	diversity of molecular determinants of binding affinity and specificity
	observed for proteins and we discuss some of the challenges that
	they pose for molecular modelling and simulation.},
  doi = {10.1016/j.bbapap.2005.07.044},
  institution = {Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg
	33, 69118 Heidelberg, Germany. rebecca.wade@eml-r.villa-bosch.de},
  keywords = {Binding Sites; Computational Biology; Cytochrome P-450 Enzyme System;
	Ligands; Models, Chemical; Models, Molecular; Protein Binding; Protein
	Structure, Tertiary; Proteins; Structure-Activity Relationship; Substrate
	Specificity},
  owner = {emilio},
  pii = {S1570-9639(05)00308-0},
  pmid = {16226496},
  timestamp = {2010.09.07},
  url = {http://dx.doi.org/10.1016/j.bbapap.2005.07.044}
}

@ARTICLE{Wade2004,
  author = {Rebecca C Wade and Peter J Winn and Ilme Schlichting and Sudarko},
  title = {A survey of active site access channels in cytochromes P450.},
  journal = {J Inorg Biochem},
  year = {2004},
  volume = {98},
  pages = {1175--1182},
  number = {7},
  month = {Jul},
  abstract = {In cytochrome P450s, the active site is situated deep inside the protein
	next to the heme cofactor, and is often completely isolated from
	the surrounding solvent. To identify routes by which substrates may
	enter into and products exit from the active site, random expulsion
	molecular dynamics simulations were performed for three cytochrome
	P450s: CYP101, CYP102A1 and CYP107A1 [J. Mol. Biol. 303 (2000) 797;
	Proc. Natl. Acad. Sci. USA 99 (2002) 5361]. Amongst the different
	pathways identified, one pathway was found to be common to all three
	cytochrome P450s although the mechanism of ligand passage along it
	was different in each case and apparently adapted to the substrate
	specificity of the enzyme. Recently, a number of new crystal structures
	of cytochrome P450s have been solved. Here, we analyse the open channels
	leading to the active site that these structures reveal. We find
	that in addition to showing the common pathway, they provide experimental
	evidence for the existence of three additional channels that were
	identified by simulation. We also discuss how the location of xenon
	binding sites in CYP101 suggests a role for one of the pathways identified
	by molecular dynamics simulations as a route for gaseous species,
	such as oxygen, to access the active site.},
  doi = {10.1016/j.jinorgbio.2004.02.007},
  institution = {Molecular and Cellular Modeling, EML Research, Villa Bosch, Schloss-Wolfsbrunnenweg
	33, 69118, Heidelberg, Germany. rebecca.wade@eml-r.villa-bosch.de},
  keywords = {Animals; Binding Sites; Crystallography, X-Ray; Cytochrome P-450 Enzyme
	System; Heme; Humans; Protein Structure, Tertiary},
  owner = {emilio},
  pii = {S0162013404000431},
  pmid = {15219983},
  timestamp = {2010.09.07},
  url = {http://dx.doi.org/10.1016/j.jinorgbio.2004.02.007}
}

@BOOK{NBS,
  title = {Journal of Physical Chemistry Reference Data: NBS Tables of Chemical
	Thermodynamic Properties},
  publisher = {American Institute of Physics, Inc.},
  year = {1982},
  author = {Wagman, D. D. and Evans, W. H. and Parker, V. B. and Schumm, R. H.
	and Halow, I. and Bailey, S. M. and Churney, K. L. and Nuttall, R.
	L.},
  address = {New York},
  optnumber = {Suppl. 2},
  optvolume = {11},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wagoner:Baker:2006,
  author = {Wagoner, J. and Baker, {N. A.}},
  title = {Assessing implicit models for nonpolar mean solvation forces: The
	importance of dispersion and volume terms},
  journal = {Proc. Natl. Acad. Sci.},
  year = {2006},
  volume = {103},
  pages = {8331--8336},
  owner = {emilio},
  timestamp = {2010.10.28}
}

@ARTICLE{Wallace:89,
  author = {Wallace, D. C.},
  journal = {Phys. Rev. A},
  year = {1989},
  volume = {39},
  pages = {4843},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wallace:87,
  author = {Wallace, D. C.},
  journal = {J. Chem. Phys.},
  year = {1987},
  volume = {87},
  pages = {2282},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wallqvist:93,
  author = {Wallqvist, A.},
  journal = {Mol. Simul.},
  year = {1993},
  volume = {10},
  pages = {13-25},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wallqvist:91,
  author = {Wallqvist, A.},
  title = {Molecular Dynamics Study of a Hydrophobic Aggregate in an Aqueous
	Solutions of Methane},
  journal = {J. Phys. Chem.},
  year = {1991},
  volume = {95},
  pages = {8921-27},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wallqvist:Berne:95,
  author = {Wallqvist, A. and Berne, B. J.},
  title = {Computer Simulation of Hydrophobic Hydration Forces on Stacked Plates
	at Short Range},
  journal = {J. Phys. Chem.},
  year = {1995},
  volume = {99},
  pages = {2893-2899},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wallqvist:Berne:94,
  author = {Wallqvist, A. and Berne, B. J.},
  title = {Molecular Dynamics Study of the Dependence of Water Solvation Free
	Energy on Solute Curvature and Surface Area},
  journal = {J. Phys. Chem.},
  year = {1994},
  volume = {99},
  pages = {2885-2892},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wallqvist:Berne:88,
  author = {Wallqvist, A. and Berne, B. J.},
  title = {Hydrophobic Interaction between a Methane Molecule and a Paraffin
	Wall in Liquid Water},
  journal = {Chem. Phys. Lett.},
  year = {1988},
  volume = {145},
  pages = {26},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wallqvist:Covell:96,
  author = {Wallqvist, A. and Covell, D. G.},
  title = {On the Origins of the Hydrophobic Effect: Observations from Simulations
	of n-Dodecane in Model Solvents.},
  journal = {Biophys. J.},
  year = {1996},
  volume = {71},
  pages = {600-608},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wallqvist:Covell:95,
  author = {Wallqvist, A. and Covell, D. G.},
  title = {Free-Energy Cost of Bending n-Dodecane in Aqueous Solution. influence
	of the Hydrophobic Effect and Solvent Exposed Area},
  journal = {J. Phys. Chem.},
  year = {1995},
  volume = {99},
  pages = {13118-13125},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@INCOLLECTION{Wallqvist:Gallicchio:Felts:Levy:2001,
  author = {Wallqvist, A. and Gallicchio, E. and Felts, A. K. and Levy, R. M.},
  title = {Detecting Native Protein Folds Among Large Decoy Sets with the OPLS
	All-Atom Potential and the Surface Generalized Born Solvent Model},
  booktitle = {Computational Methods for Protein Folding: A Special Volume of Advances
	in Chemical Physics},
  publisher = {John Wiley \& Sons},
  year = {2002},
  editor = {R. Friesner},
  volume = {120},
  series = {Adv. Chem. Phys.},
  pages = {459-486},
  address = {New York},
  note = {I. Prigogine and S.A. Rice, series editors},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wallqvist:Gallicchio:Levy:2001,
  author = {Wallqvist, A. and Gallicchio, E. and Levy, R. M.},
  title = {A model for studying drying at hydrophobic interfaces: structural
	and thermodynamic properties},
  journal = {J. Phys. Chem. B},
  year = {2001},
  volume = {105},
  pages = {6745-6753},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wang2006,
  author = {Jiyao Wang and Yuqing Deng and Beno\^{i}t Roux},
  title = {Absolute binding free energy calculations using molecular dynamics
	simulations with restraining potentials.},
  journal = {Biophys. J.},
  year = {2006},
  volume = {91},
  pages = {2798--2814},
  number = {8},
  month = {Oct},
  abstract = {The absolute (standard) binding free energy of eight FK506-related
	ligands to FKBP12 is calculated using free energy perturbation molecular
	dynamics (FEP/MD) simulations with explicit solvent. A number of
	features are implemented to improve the accuracy and enhance the
	convergence of the calculations. First, the absolute binding free
	energy is decomposed into sequential steps during which the ligand-surrounding
	interactions as well as various biasing potentials restraining the
	translation, orientation, and conformation of the ligand are turned
	"on" and "off." Second, sampling of the ligand conformation is enforced
	by a restraining potential based on the root mean-square deviation
	relative to the bound state conformation. The effect of all the restraining
	potentials is rigorously unbiased, and it is shown explicitly that
	the final results are independent of all artificial restraints. Third,
	the repulsive and dispersive free energy contribution arising from
	the Lennard-Jones interactions of the ligand with its surrounding
	(protein and solvent) is calculated using the Weeks-Chandler-Andersen
	separation. This separation also improves convergence of the FEP/MD
	calculations. Fourth, to decrease the computational cost, only a
	small number of atoms in the vicinity of the binding site are simulated
	explicitly, while all the influence of the remaining atoms is incorporated
	implicitly using the generalized solvent boundary potential (GSBP)
	method. With GSBP, the size of the simulated FKBP12/ligand systems
	is significantly reduced, from approximately 25,000 to 2500. The
	computations are very efficient and the statistical error is small
	( approximately 1 kcal/mol). The calculated binding free energies
	are generally in good agreement with available experimental data
	and previous calculations (within approximately 2 kcal/mol). The
	present results indicate that a strategy based on FEP/MD simulations
	of a reduced GSBP atomic model sampled with conformational, translational,
	and orientational restraining potentials can be computationally inexpensive
	and accurate.},
  doi = {10.1529/biophysj.106.084301},
  institution = {Institute of Molecular Pediatric Sciences, Gordon Center for Integrative
	Science, University of Chicago, Chicago, Illinois, USA.},
  keywords = {Computer Simulation; Ligands; Models, Molecular; Protein Binding;
	Protein Conformation; Tacrolimus; Tacrolimus Binding Protein 1A;
	Thermodynamics},
  owner = {emilio},
  pii = {S0006-3495(06)71994-4},
  pmid = {16844742},
  timestamp = {2010.04.27},
  url = {http://dx.doi.org/10.1529/biophysj.106.084301}
}

@ARTICLE{Wang:Dixon:Kollman:1999,
  author = {Wang, J. and Dixon, R. and Kollman, {P. A.}},
  title = {Ranking Ligand Binding Affinities With Avidin: A Molecular Dynamics-Based
	Interaction Energy Study},
  journal = {Proteins Struct. Funct. Genet.},
  year = {1999},
  volume = {34},
  pages = {69--81},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wang2011,
  author = {Wang, Jin and Wang, Yong and Chu, Xiakun and Hagen, Stephen J. and
	Han, Wei and Wang, Erkang},
  title = {Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically
	Disordered Protein Inhibitor IA3 to its Target Enzyme},
  journal = {PLoS Comput Biol},
  year = {2011},
  volume = {7},
  pages = {e1001118},
  number = {4},
  month = {Apr},
  abstract = {<title>Author Summary</title> <p>The intrinsically disordered peptide
	IA3 is the endogenous inhibitor for the enzyme named yeast aspartic
	proteinase saccharopepsin (YPrA). In the presence of YPrA, IA3 folds
	itself into an amphipathic helix that blocks the active site cleft
	of the enzyme. We developed a multi-scaled approach to explore the
	underlying mechanism of this binding-induced ordering transition.
	Our approach combines a structure-based molecular dynamics model
	at the residue level with a stochastic path method at the atomic
	level. Our simulations suggest that IA3 inhibits YPrA through an
	induced-fit mechanism where the enzyme (YPrA) induces conformational
	change of its inhibitor (IA3). This expands the definition of an
	induced-fit model from its original meaning that the binding of substrate
	(IA3) drives conformational change in the protein (YPrA). Our result
	is consistent with recent kinetic experiments and provides a microscopic
	explanation for the underlying mechanism. We also discuss the important
	roles of non-native interactions and backtracking. These results
	enrich our understanding of the enzyme-inhibition mechanism and may
	have value in the design of drugs.</p>},
  owner = {emilio},
  publisher = {Public Library of Science},
  timestamp = {2011.07.15},
  url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1001118}
}

@ARTICLE{Wang2009,
  author = {Lingle Wang and Robert Abel and Richard A Friesner and B. J. Berne},
  title = {Thermodynamic properties of liquid water: an application of a nonparametric
	approach to computing the entropy of a neat fluid.},
  journal = {J Chem Theory Comput},
  year = {2009},
  volume = {5},
  pages = {1462--1473},
  number = {6},
  month = {Jun},
  abstract = {Due to its fundamental importance to molecular biology, great interest
	has continued to persist in developing novel techniques to efficiently
	characterize the thermodynamic and structural features of liquid
	water. A particularly fruitful approach, first applied to liquid
	water by Lazaridis and Karplus, is to use molecular dynamics or Monte
	Carlo simulations to collect the required statistics to integrate
	the inhomogeneous solvation theory equations for the solvation enthalpy
	and entropy. We here suggest several technical improvements to this
	approach, which may facilitate faster convergence and greater accuracy.
	In particular, we devise a nonparametric k'th nearest neighbors (NN)
	based approach to estimate the water-water correlation entropy, and
	suggest an alternative factorization of the water-water correlation
	function that appears to more robustly describe the correlation entropy
	of the neat fluid. It appears that the NN method offers several advantages
	over the more common histogram based approaches, including much faster
	convergence for a given amount of simulation data; an intuitive error
	bound that may be readily formulated without resorting to block averaging
	or bootstrapping; and the absence of empirically tuned parameters,
	which may bias the results in an uncontrolled fashion.},
  doi = {10.1021/ct900078k},
  institution = {Department of Chemistry, Columbia University, New York, NY, 10027,
	bb8@columbia.edu.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {19851475},
  timestamp = {2012.06.21},
  url = {http://dx.doi.org/10.1021/ct900078k}
}

@ARTICLE{Wang2012,
  author = {Wang, Lingle and Berne, B. J. and Friesner, Richard A.},
  title = {On achieving high accuracy and reliability in the calculation of
	relative protein-ligand binding affinities},
  journal = {Proc. Natl. Acad. Sci.},
  year = {2012},
  volume = {109},
  pages = {1937--1942},
  number = {6},
  abstract = {We apply a free energy perturbation simulation method, free energy
	perturbation/replica exchange with solute tempering, to two modifications
	of protein–ligand complexes that lead to significant conformational
	changes, the first in the protein and the second in the ligand. The
	approach is shown to facilitate sampling in these challenging cases
	where high free energy barriers separate the initial and final conformations
	and leads to superior convergence of the free energy as demonstrated
	both by consistency of the results (independence from the starting
	conformation) and agreement with experimental binding affinity data.
	The second case, consisting of two neutral thrombin ligands that
	are taken from a recent medicinal chemistry program for this interesting
	pharmaceutical target, is of particular significance in that it demonstrates
	that good results can be obtained for large, complex ligands, as
	opposed to relatively simple model systems. To achieve quantitative
	agreement with experiment in the thrombin case, a next generation
	force field, Optimized Potentials for Liquid Simulations 2.0, is
	required, which provides superior charges and torsional parameters
	as compared to earlier alternatives.},
  date = {February 7, 2012},
  doi = {10.1073/pnas.1114017109},
  owner = {emilio},
  timestamp = {2012.06.20},
  url = {http://www.pnas.org/content/109/6/1937.abstract}
}

@ARTICLE{Wang2012a,
  author = {Lingle Wang and B. J. Berne and Richard A Friesner},
  title = {On achieving high accuracy and reliability in the calculation of
	relative protein-ligand binding affinities.},
  journal = {Proc Natl Acad Sci U S A},
  year = {2012},
  volume = {109},
  pages = {1937--1942},
  number = {6},
  month = {Feb},
  abstract = {We apply a free energy perturbation simulation method, free energy
	perturbation/replica exchange with solute tempering, to two modifications
	of protein-ligand complexes that lead to significant conformational
	changes, the first in the protein and the second in the ligand. The
	approach is shown to facilitate sampling in these challenging cases
	where high free energy barriers separate the initial and final conformations
	and leads to superior convergence of the free energy as demonstrated
	both by consistency of the results (independence from the starting
	conformation) and agreement with experimental binding affinity data.
	The second case, consisting of two neutral thrombin ligands that
	are taken from a recent medicinal chemistry program for this interesting
	pharmaceutical target, is of particular significance in that it demonstrates
	that good results can be obtained for large, complex ligands, as
	opposed to relatively simple model systems. To achieve quantitative
	agreement with experiment in the thrombin case, a next generation
	force field, Optimized Potentials for Liquid Simulations 2.0, is
	required, which provides superior charges and torsional parameters
	as compared to earlier alternatives.},
  doi = {10.1073/pnas.1114017109},
  institution = {Department of Chemistry, Columbia University, 3000 Broadway, New
	York, NY 10027, USA.},
  keywords = {Acetamides, metabolism; Bacteriophage T4, enzymology; Benzene, metabolism;
	Binding Sites; Computer Simulation; Crystallography, X-Ray; Ligands;
	Models, Molecular; Muramidase, chemistry/metabolism; Mutant Proteins,
	metabolism; Protein Binding; Protein Conformation; Proteins, metabolism;
	Thermodynamics; Thrombin, chemistry/metabolism; Valine, metabolism;
	Xylenes, metabolism},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {1114017109},
  pmid = {22308365},
  timestamp = {2012.06.21},
  url = {http://dx.doi.org/10.1073/pnas.1114017109}
}

@ARTICLE{Wang2011c,
  author = {Lingle Wang and B. J. Berne and R. A. Friesner},
  title = {Ligand binding to protein-binding pockets with wet and dry regions.},
  journal = {Proc Natl Acad Sci U S A},
  year = {2011},
  volume = {108},
  pages = {1326--1330},
  number = {4},
  month = {Jan},
  abstract = {Biological processes often depend on protein-ligand binding events,
	yet accurate calculation of the associated energetics remains as
	a significant challenge of central importance to structure-based
	drug design. Recently, we have proposed that the displacement of
	unfavorable waters by the ligand, replacing them with groups complementary
	to the protein surface, is the principal driving force for protein-ligand
	binding, and we have introduced the WaterMap method to account this
	effect. However, in spite of the adage "nature abhors vacuum," one
	can occasionally observe situations in which a portion of the receptor
	active site is so unfavorable for water molecules that a void is
	formed there. In this paper, we demonstrate that the presence of
	dry regions in the receptor has a nontrivial effect on ligand binding
	affinity, and suggest that such regions may represent a general motif
	for molecular recognition between the dry region in the receptor
	and the hydrophobic groups in the ligands. With the introduction
	of a term attributable to the occupation of the dry regions by ligand
	atoms, combined with the WaterMap calculation, we obtain excellent
	agreement with experiment for the prediction of relative binding
	affinities for a number of congeneric ligand series binding to the
	major urinary protein receptor. In addition, WaterMap when combined
	with the cavity contribution is more predictive than at least one
	specific implementation [Abel R, Young T, Farid R, Berne BJ, Friesner
	RA (2008) J Am Chem Soc 130:2817-2831] of the popular MM-GBSA approach
	to binding affinity calculation.},
  doi = {10.1073/pnas.1016793108},
  institution = {Department of Chemistry, Columbia University, 3000 Broadway, New
	York, NY 10027, USA.},
  keywords = {Algorithms; Animals; Binding Sites; Binding, Competitive; Computational
	Biology, methods; Entropy; Kinetics; Ligands; Mice; Models, Chemical;
	Models, Molecular; Molecular Structure; Protein Binding; Protein
	Structure, Tertiary; Proteins, chemistry/metabolism; Water, chemistry/metabolism},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {1016793108},
  pmid = {21205906},
  timestamp = {2012.06.21},
  url = {http://dx.doi.org/10.1073/pnas.1016793108}
}

@ARTICLE{Wang2011a,
  author = {Wang, Lingle and Friesner, Richard A. and Berne, B. J.},
  title = {Replica Exchange with Solute Scaling: A More Efficient Version of
	Replica Exchange with Solute Tempering (REST2)},
  journal = {J. Phys. Chem. B},
  year = {2011},
  volume = {115},
  pages = {9431--9438},
  number = {30},
  month = jun,
  abstract = {A small change in the Hamiltonian scaling in Replica Exchange with
	Solute Tempering (REST) is found to improve its sampling efficiency
	greatly, especially for the sampling of aqueous protein solutions
	in which there are large-scale solute conformation changes. Like
	the original REST (REST1), the new version (which we call REST2)
	also bypasses the poor scaling with system size of the standard Temperature
	Replica Exchange Method (TREM), reducing the number of replicas (parallel
	processes) from what must be used in TREM. This reduction is accomplished
	by deforming the Hamiltonian function for each replica in such a
	way that the acceptance probability for the exchange of replica configurations
	does not depend on the number of explicit water molecules in the
	system. For proof of concept, REST2 is compared with TREM and with
	REST1 for the folding of the trpcage and ?-hairpin in water. The
	comparisons confirm that REST2 greatly reduces the number of CPUs
	required by regular replica exchange and greatly increases the sampling
	efficiency over REST1. This method reduces the CPU time required
	for calculating thermodynamic averages and for the ab initio folding
	of proteins in explicit water.

	A small change in the Hamiltonian scaling in Replica Exchange with
	Solute Tempering (REST) is found to improve its sampling efficiency
	greatly, especially for the sampling of aqueous protein solutions
	in which there are large-scale solute conformation changes. Like
	the original REST (REST1), the new version (which we call REST2)
	also bypasses the poor scaling with system size of the standard Temperature
	Replica Exchange Method (TREM), reducing the number of replicas (parallel
	processes) from what must be used in TREM. This reduction is accomplished
	by deforming the Hamiltonian function for each replica in such a
	way that the acceptance probability for the exchange of replica configurations
	does not depend on the number of explicit water molecules in the
	system. For proof of concept, REST2 is compared with TREM and with
	REST1 for the folding of the trpcage and ?-hairpin in water. The
	comparisons confirm that REST2 greatly reduces the number of CPUs
	required by regular replica exchange and greatly increases the sampling
	efficiency over REST1. This method reduces the CPU time required
	for calculating thermodynamic averages and for the ab initio folding
	of proteins in explicit water.},
  booktitle = {The Journal of Physical Chemistry B},
  comment = {doi: 10.1021/jp204407d},
  issn = {1520-6106},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.09.27},
  url = {http://pubs.acs.org/doi/abs/10.1021/jp204407d}
}

@ARTICLE{Wang2011b,
  author = {Lingle Wang and Richard A Friesner and B. J. Berne},
  title = {Replica exchange with solute scaling: a more efficient version of
	replica exchange with solute tempering (REST2).},
  journal = {J Phys Chem B},
  year = {2011},
  volume = {115},
  pages = {9431--9438},
  number = {30},
  month = {Aug},
  abstract = {A small change in the Hamiltonian scaling in Replica Exchange with
	Solute Tempering (REST) is found to improve its sampling efficiency
	greatly, especially for the sampling of aqueous protein solutions
	in which there are large-scale solute conformation changes. Like
	the original REST (REST1), the new version (which we call REST2)
	also bypasses the poor scaling with system size of the standard Temperature
	Replica Exchange Method (TREM), reducing the number of replicas (parallel
	processes) from what must be used in TREM. This reduction is accomplished
	by deforming the Hamiltonian function for each replica in such a
	way that the acceptance probability for the exchange of replica configurations
	does not depend on the number of explicit water molecules in the
	system. For proof of concept, REST2 is compared with TREM and with
	REST1 for the folding of the trpcage and β-hairpin in water. The
	comparisons confirm that REST2 greatly reduces the number of CPUs
	required by regular replica exchange and greatly increases the sampling
	efficiency over REST1. This method reduces the CPU time required
	for calculating thermodynamic averages and for the ab initio folding
	of proteins in explicit water.},
  doi = {10.1021/jp204407d},
  institution = {Department of Chemistry, Columbia University, 3000 Broadway, New
	York, New York 10027, United States.},
  keywords = {Protein Folding; Protein Structure, Secondary; Proteins, chemistry;
	Temperature; Thermodynamics; Water, chemistry},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {21714551},
  timestamp = {2012.06.21},
  url = {http://dx.doi.org/10.1021/jp204407d}
}

@ARTICLE{Wang2010,
  author = {Lingle Wang and Richard A Friesner and B. J. Berne},
  title = {Competition of electrostatic and hydrophobic interactions between
	small hydrophobes and model enclosures.},
  journal = {J Phys Chem B},
  year = {2010},
  volume = {114},
  pages = {7294--7301},
  number = {21},
  month = {Jun},
  abstract = {The binding affinity between a probe hydrophobic particle and model
	hydrophobic plates with different charge (or dipole) densities in
	water was investigated through molecular dynamics simulation free-energy
	perturbation calculations. We observed a reduced binding affinity
	when the plates are charged, in agreement with previous findings.
	With increased charge density, the plates can change from "hydrophobic
	like" (pulling the particle into the interplate region) to "hydrophilic
	like" (ejecting the particle out of the interplate region), demonstrating
	the competition between hydrophobic and electrostatic interactions.
	The reduction of the binding affinity is quadratically dependent
	on the magnitude of the charge for symmetric systems, but linear
	and cubic terms also make a contribution for asymmetric systems.
	Statistical perturbation theory explains these results and shows
	when and why implicit solvent models fail.},
  doi = {10.1021/jp100772w},
  institution = {Department of Chemistry, Columbia University, 3000 Broadway, New
	York, New York 10027, USA.},
  keywords = {Hydrophobicity; Models, Molecular; Solvents; Static Electricity; Thermodynamics;
	Water},
  owner = {emilio},
  pmid = {20443643},
  timestamp = {2010.10.28},
  url = {http://dx.doi.org/10.1021/jp100772w}
}

@ARTICLE{Wang2010a,
  author = {Lingle Wang and Richard A Friesner and B. J. Berne},
  title = {Hydrophobic interactions in model enclosures from small to large
	length scales: non-additivity in explicit and implicit solvent models.},
  journal = {Faraday Discuss},
  year = {2010},
  volume = {146},
  pages = {247--62; discussion 283-98, 395-401},
  abstract = {The binding affinities between a united-atom methane and various model
	hydrophobic enclosures were studied through high accuracy free energy
	perturbation methods (FEP). We investigated the non-additivity of
	the hydrophobic interaction in these systems, measured by the deviation
	of its binding affinity from that predicted by the pairwise additivity
	approximation. While only small non-additivity effects were previously
	reported in the interactions in methane trimers, we found large cooperative
	effects (as large as -1.14 kcal mol(-1) or approximately a 25\% increase
	in the binding affinity) and anti-cooperative effects (as large as
	0.45 kcal mol(-1)) for these model enclosed systems. Decomposition
	of the total potential of mean force (PMF) into increasing orders
	of multi-body interactions indicates that the contributions of the
	higher order multi-body interactions can be either positive or negative
	in different systems, and increasing the order of multi-body interactions
	considered did not necessarily improve the accuracy. A general correlation
	between the sign of the non-additivity effect and the curvature of
	the solute molecular surface was observed. We found that implicit
	solvent models based on the molecular surface area (MSA) performed
	much better, not only in predicting binding affinities, but also
	in predicting the non-additivity effects, compared with models based
	on the solvent accessible surface area (SASA), suggesting that MSA
	is a better descriptor of the curvature of the solutes. We also show
	how the non-additivity contribution changes as the hydrophobicity
	of the plate is decreased from the dewetting regime to the wetting
	regime.},
  institution = {Department of Chemistry, Columbia University, 3000 Broadway, New
	York, NY 10027, USA.},
  keywords = {Hydrophobic and Hydrophilic Interactions; Methane, chemistry; Molecular
	Dynamics Simulation; Solvents, chemistry},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {21043426},
  timestamp = {2012.06.21}
}

@ARTICLE{Wang:Hermans:95,
  author = {Wang, L. and Hermans, J.},
  journal = {J. Phys. Chem.},
  year = {1995},
  volume = {99},
  pages = {12001-12007},
  owner = {emilio},
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repository: radical-papers/radical-references

repo_name: radical-papers/radical-references