Applications of free energy calculations to chemistry and biology

[1]  P. Hünenberger,et al.  Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines , 2001 .

[2]  G. Hummer,et al.  Computer simulations do not support Cl-Cl pairing in aqueous NaCl solution , 1994 .

[3]  Arieh Warshel,et al.  Free-Energy Perturbation Calculations of DNA Destabilization by Base Substitutions: The Effect of Neutral Guanine·Thymine, Adenine·Cytosine and Adenine·Difluorotoluene Mismatches , 2000 .

[4]  G. Voth,et al.  Free energy profiles for H+ conduction in the D-pathway of Cytochrome c Oxidase: a study of the wild type and N98D mutant enzymes. , 2006, Biochimica et biophysica acta.

[5]  E. Overton.  Studien über die Narkose : zugleich ein Beitrag zur allgemeinen Pharmakologie , 1901 .

[6]  D. Case,et al.  Constant pH molecular dynamics in generalized Born implicit solvent , 2004, J. Comput. Chem..

[7]  A. Fersht.  Structure and mechanism in protein science , 1998 .

[8]  Shaomeng Wang,et al.  Helix Folding of an Alanine-Based Peptide in Explicit Water , 2001 .

[9]  Christophe Chipot,et al.  Rational determination of transfer free energies of small drugs across the water-oil interface. , 2002, Journal of medicinal chemistry.

[10]  Vijay S. Pande,et al.  Screen Savers of the World Unite! , 2000, Science.

[11]  Klaus Schulten,et al.  Steered Molecular Dynamics , 1999, Computational Molecular Dynamics.

[12]  Justin L. MacCallum,et al.  Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field , 2003, J. Comput. Chem..

[13]  V. Luzhkov,et al.  Ion permeation mechanism of the potassium channel , 2000, Nature.

[14]  Reinskje Talhout,et al.  Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin. , 2003, Journal of the American Chemical Society.

[15]  William L. Jorgensen,et al.  Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model , 1994 .

[16]  H. Nymeyer,et al.  Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[17]  William L. Jorgensen,et al.  OPLS ALL-ATOM MODEL FOR AMINES : RESOLUTION OF THE AMINE HYDRATION PROBLEM , 1999 .

[18]  Stefan Boresch,et al.  Absolute Binding Free Energies: A Quantitative Approach for Their Calculation , 2003 .

[19]  K. Sanbonmatsu,et al.  Structure of Met‐enkephalin in explicit aqueous solution using replica exchange molecular dynamics , 2002, Proteins.

[20]  Richard H. Henchman,et al.  Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. , 2004, Biophysical journal.

[21]  Alan M. Ferrenberg,et al.  Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.

[22]  A. Pohorille,et al.  Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A , 2005 .

[23]  Donald Hamelberg,et al.  Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. , 2004, Journal of the American Chemical Society.

[24]  L. Pratt.  Molecular theory of hydrophobic effects: "She is too mean to have her name repeated.". , 2001, Annual review of physical chemistry.

[25]  W. Im,et al.  Generalized solvent boundary potential for computer simulations , 2001 .

[26]  Chris Oostenbrink,et al.  A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..

[27]  S. Lifson,et al.  On the Theory of Helix—Coil Transition in Polypeptides , 1961 .

[28]  Thomas Simonson,et al.  Gaussian fluctuations and linear response in an electron transfer protein , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Arieh Warshel,et al.  A local reaction field method for fast evaluation of long‐range electrostatic interactions in molecular simulations , 1992 .

[30]  T. Darden,et al.  Molecular dynamics simulations of biomolecules: long-range electrostatic effects. , 1999, Annual review of biophysics and biomolecular structure.

[31]  V Daggett,et al.  Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding. , 2001, Biochemistry.

[32]  C. Brooks,et al.  From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. , 2001, Annual review of physical chemistry.

[33]  William L. Jorgensen,et al.  Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water , 1988 .

[34]  T. Straatsma,et al.  Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water , 1986 .

[35]  Thomas Simonson,et al.  Conformational substrates and uncertainty in macromolecular free energy calculations , 1993 .

[36]  M Karplus,et al.  Free energy simulations: The meaning of the individual contributions from a component analysis , 1994, Proteins.

[37]  M. Karplus,et al.  Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. , 1989, Science.

[38]  A Mitsutake,et al.  Generalized-ensemble algorithms for molecular simulations of biopolymers. , 2000, Biopolymers.

[39]  Seokmin Shin,et al.  Replica-exchange method using the generalized effective potential. , 2003, Physical review letters.

[40]  P. Bandyopadhyay,et al.  Evidence for an umbrella mechanism of bilayer transport. , 2001, Journal of the American Chemical Society.

[41]  Jeremy C. Smith,et al.  Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. , 1996, Biophysical journal.

[42]  Thomas Simonson,et al.  Free energy simulations come of age: protein-ligand recognition. , 2002, Accounts of chemical research.

[43]  Terry R. Stouch,et al.  Orientation and Diffusion of a Drug Analog in Biomembranes: Molecular Dynamics Simulations , 1995 .

[44]  M. Klein,et al.  Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer. , 1998, Biophysical journal.

[45]  B. Roux,et al.  Energetics of ion conduction through the gramicidin channel , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Tony F. Heinz,et al.  Studies of Liquid Surfaces by Second Harmonic Generation , 1986 .

[47]  A T Brünger,et al.  Proline cis‐trans isomerization in staphylococcal nuclease: Multi‐substate free energy perturbation calculations , 1995, Protein science : a publication of the Protein Society.

[48]  B. Tidor.  Helix‐capping interaction in λ cro protein: A free energy simulation analysis , 1994 .

[49]  Vijay S Pande,et al.  Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. , 2004, The Journal of chemical physics.

[50]  G. D. Billing.  Mixed Quantum–Classical Methods , 2002 .

[51]  D. L. Veenstra,et al.  Free energy calculations of the mutation of Ile96-->Ala in barnase: contributions to the difference in stability. , 1996, Protein engineering.

[52]  S. Zographos,et al.  Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues , 2005, Proteins.

[53]  Arieh Warshel,et al.  Computer Modeling of Chemical Reactions in Enzymes and Solutions , 1991 .

[54]  K. Schulten,et al.  Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning , 2002, Science.

[55]  P. Tavan,et al.  Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force , 1996, Science.

[56]  Adrian J Mulholland,et al.  Modelling enzyme reaction mechanisms, specificity and catalysis. , 2005, Drug discovery today.

[57]  V. Pande,et al.  Multiplexed-replica exchange molecular dynamics method for protein folding simulation. , 2003, Biophysical journal.

[58]  Kenneth M. Merz,et al.  Free Energy Perturbation Study of Octanol/Water Partition Coefficients: Comparison with Continuum GB/SA Calculations , 1999 .

[59]  K. Strømgaard,et al.  Site‐Specific Incorporation of Unnatural Amino Acids into Proteins , 2004, Chembiochem : a European journal of chemical biology.

[60]  Solvated chloride ions at contact , 1987 .

[61]  Jonathan W. Essex,et al.  Theoretical determination of partition coefficients , 1992 .

[62]  P A Kollman,et al.  What determines the strength of noncovalent association of ligands to proteins in aqueous solution? , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[63]  Peter L. Cummins,et al.  Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation , 2005, J. Comput. Chem..

[64]  W F van Gunsteren,et al.  Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies. , 1994, Journal of molecular biology.

[65]  Peter A. Kollman,et al.  Molecular Dynamics Potential of Mean Force Calculations: A Study of the Toluene−Ammonium π-Cation Interactions , 1996 .

[66]  William L. Jorgensen,et al.  Free Energies of Hydration for Organic Molecules from Monte Carlo Simulations , 1995 .

[67]  Benoît Roux,et al.  Theoretical and computational models of ion channels. , 2002, Current opinion in structural biology.

[68]  H. Qian,et al.  Helix-coil theories: a comparative study for finite length polypeptides , 1992 .

[69]  Peter A. Kollman,et al.  Solvation Free Energies of Amides and Amines: Disagreement between Free Energy Calculations and Experiment , 1995 .

[70]  Luis Moroder,et al.  Modeled structure of a G-protein-coupled receptor: the cholecystokinin-1 receptor. , 2005, Journal of medicinal chemistry.

[71]  M Karplus,et al.  Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. , 2001, Journal of molecular biology.

[72]  G. Torrie,et al.  Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .

[73]  C L Brooks,et al.  Calculations on folding of segment B1 of streptococcal protein G. , 1998, Journal of molecular biology.

[74]  D. Beglov,et al.  Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations , 1994 .

[75]  Charles L. Brooks,et al.  Molecular picture of folding of a small α/β protein , 1998 .

[76]  A. Pohorille,et al.  Molecular modeling of protocellular functions. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[77]  M. Gilson,et al.  The statistical-thermodynamic basis for computation of binding affinities: a critical review. , 1997, Biophysical journal.

[78]  Arieh Warshel,et al.  Exploring the origin of the ion selectivity of the KcsA potassium channel , 2003, Proteins.

[79]  Gerhard Hummer,et al.  Free Energy of Ionic Hydration , 1996 .

[80]  Joan-Emma Shea,et al.  Probing the folding free energy landscape of the src-SH3 protein domain , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[81]  Alessandra Villa,et al.  Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin , 2003, J. Comput. Aided Mol. Des..

[82]  J. Kirsch,et al.  Energetic analysis of an antigen/antibody interface: Alanine scanning mutagenesis and double mutant cycles on the hyhel‐10/lysozyme interaction , 1999, Protein science : a publication of the Protein Society.

[83]  Peter A. Kollman,et al.  Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions , 1996, J. Comput. Chem..

[84]  Peter A. Kollman,et al.  Free energy calculations on protein stability: Thr-157 .fwdarw. Val-157 mutation of T4 lysozyme , 1989 .

[85]  William L. Jorgensen,et al.  Accuracy of free energies of hydration using CM1 and CM3 atomic charges , 2004, J. Comput. Chem..

[86]  Alessandra Villa,et al.  Calculation of the free energy of solvation for neutral analogs of amino acid side chains , 2002, J. Comput. Chem..

[87]  K. Schulten,et al.  What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF. , 2005, Structure.

[88]  B. Roux.  The Art of Dissecting the Function of a Potassium Channel , 2005, Neuron.

[89]  P. Marlière,et al.  Artificially ambiguous genetic code confers growth yield advantage. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[90]  Qiang Cui,et al.  Free energy perturbation calculations with combined QM/MM potentials complications, simplifications, and applications to redox potential calculations , 2003 .

[91]  T. Simonson,et al.  Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model. , 2001, Journal of the American Chemical Society.

[92]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , 1997 .

[93]  B. Roux,et al.  Calculation of absolute protein-ligand binding free energy from computer simulations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[94]  Bruce J. Berne,et al.  A Monte Carlo simulation of the hydrophobic interaction , 1979 .

[95]  Alan E. Mark,et al.  Estimating the Relative Free Energy of Different Molecular States with Respect to a Single Reference State , 1996 .

[96]  Klaus Schulten,et al.  Molecular dynamics simulations of proteins in lipid bilayers. , 2005, Current opinion in structural biology.

[97]  C. Brooks,et al.  Calculation of free energy surfaces using the methods of thermodynamic perturbation theory , 1987 .

[98]  Wilfred F. van Gunsteren,et al.  Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , 1989 .

[99]  E. Tajkhorshid,et al.  Molecular basis of proton blockage in aquaporins. , 2004, Structure.

[100]  William L. Jorgensen,et al.  Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene , 1990 .

[101]  Christophe Chipot,et al.  Modeling ion-ion interaction in proteins: A molecular dynamics free energy calculation of the guanidinium-acetate association , 2000 .

[102]  Ronald M. Levy,et al.  SOLVATION FREE ENERGIES OF SMALL AMIDES AND AMINES FROM MOLECULAR DYNAMICS/FREE ENERGY PERTURBATION SIMULATIONS USING PAIRWISE ADDITIVE AND MANY-BODY POLARIZABLE POTENTIALS , 1995 .

[103]  J. Hermans,et al.  Excess free energy of liquids from molecular dynamics simulations. Application to water models. , 1988, Journal of the American Chemical Society.

[104]  S. Takada,et al.  On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction , 2002 .

[105]  Gregory A Voth,et al.  Computer simulation of proton solvation and transport in aqueous and biomolecular systems. , 2006, Accounts of chemical research.

[106]  N. Oppenheimer,et al.  Structure and mechanism , 1989 .

[107]  D. Case,et al.  Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models. , 2004, Journal of the American Chemical Society.

[108]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[109]  Thomas Simonson,et al.  Continuum Treatment of Long-Range Interactions in Free Energy Calculations. Application to Protein−Ligand Binding. , 1997 .

[110]  T R Stouch,et al.  Drug-membrane interactions studied by molecular dynamics simulation: size dependence of diffusion. , 1996, Drug design and discovery.

[111]  William L. Jorgensen,et al.  Hydration and energetics for tert-butyl chloride ion pairs in aqueous solution , 1987 .

[112]  Gregory A Voth,et al.  A multistate empirical valence bond description of protonatable amino acids. , 2006, The journal of physical chemistry. A.

[113]  Christophe Chipot,et al.  Can Absolute Free Energies of Association Be Estimated from Molecular Mechanical Simulations? The Biotin−Streptavidin System Revisited , 2001 .

[114]  J. Valleau,et al.  A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution , 1975 .

[115]  Kenneth M. Merz,et al.  CO2 binding to human carbonic anhydrase II , 1991 .

[116]  T. Simonson.  Electrostatic Free Energy Calculations for Macromolecules: A Hybrid Molecular Dynamics/Continuum Electrostatics Approach , 2000 .

[117]  H. Scheraga,et al.  Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[118]  P. Kollman,et al.  Investigating the Anomalous Solvation Free Energies of Amines with a Polarizable Potential , 1996 .

[119]  Y. Sugita,et al.  Multidimensional replica-exchange method for free-energy calculations , 2000, cond-mat/0009120.

[120]  A. Pohorille,et al.  Mechanism of unassisted ion transport across membrane bilayers. , 1996, Journal of the American Chemical Society.

[121]  Zhuyan Guo,et al.  Application of the lambda-dynamics method to evaluate the relative binding free energies of inhibitors to HCV protease. , 2003, Journal of medicinal chemistry.

[122]  Benedict Leimkuhler,et al.  Computational Molecular Dynamics: Challenges, Methods, Ideas , 1999, Computational Molecular Dynamics.

[123]  William L. Jorgensen,et al.  Monte Carlo simulations of pure liquid substituted benzenes with OPLS potential functions , 1993, J. Comput. Chem..

[124]  X. Daura,et al.  Parametrization of aliphatic CHn united atoms of GROMOS96 force field , 1998 .

[125]  Thomas Simonson,et al.  Protein‐protein recognition: An experimental and computational study of the R89K mutation in Raf and its effect on Ras binding , 2008, Protein science : a publication of the Protein Society.

[126]  K. Sanbonmatsu,et al.  Exploring the energy landscape of a β hairpin in explicit solvent , 2001 .

[127]  T. Ichiye,et al.  Understanding Intramolecular Electron Transfer in Ferredoxin: A Molecular Dynamics Study , 2004 .

[128]  M. Marchi,et al.  Linear response and electron transfer in complex biomolecular systems and a reaction center protein , 2003 .

[129]  X. Daura,et al.  Reversible peptide folding in solution by molecular dynamics simulation. , 1998, Journal of molecular biology.

[130]  W. L. Jorgensen.  The Many Roles of Computation in Drug Discovery , 2004, Science.

[131]  W F van Gunsteren,et al.  Can the stability of protein mutants be predicted by free energy calculations? , 1993, Protein engineering.

[132]  Benoît Roux,et al.  Grand canonical Monte Carlo simulations of water in protein environments. , 2004, The Journal of chemical physics.

[133]  J. Wendoloski,et al.  Structural origins of high-affinity biotin binding to streptavidin. , 1989, Science.

[134]  Peter A. Kollman,et al.  FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .

[135]  Chris Oostenbrink,et al.  Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site , 2005, Nucleic acids research.

[136]  Christophe Chipot,et al.  Probing a model of a GPCR/ligand complex in an explicit membrane environment: the human cholecystokinin-1 receptor. , 2006, Biophysical journal.

[137]  Christophe Chipot,et al.  Rational determination of charge distributions for free energy calculations , 2003, J. Comput. Chem..

[138]  T. Simonson,et al.  Free‐Energy Simulations and Experiments Reveal Long‐Range Electrostatic Interactions and Substrate‐Assisted Specificity in an Aminoacyl‐tRNA Synthetase , 2006, Chembiochem : a European journal of chemical biology.

[139]  C. Brooks,et al.  First-principles calculation of the folding free energy of a three-helix bundle protein. , 1995, Science.

[140]  D. N. Card,et al.  Monte Carlo Estimation of the Free Energy by Multistage Sampling , 1972 .

[141]  A. Warshel,et al.  Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. , 1986, Biochemistry.

[142]  J. Andrew McCammon,et al.  Sodium chloride ion pair interaction in water: computer simulation , 1984 .

[143]  P. A. Bash,et al.  Calculation of the relative change in binding free energy of a protein-inhibitor complex. , 1987, Science.

[144]  A. Pohorille,et al.  Molecular dynamics of phenol at the liquid-vapor interface of water. , 1991, The Journal of chemical physics.

[145]  J. Hermans,et al.  The Free Energy of Xenon Binding to Myoglobin from Molecular Dynamics Simulation , 1986 .

[146]  M. Karplus,et al.  How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations , 2004, Science.

[147]  Michael R. Shirts,et al.  Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. , 2005, The Journal of chemical physics.

[148]  Peter A. Kollman,et al.  Benzene Dimer: A Good Model for π−π Interactions in Proteins? A Comparison between the Benzene and the Toluene Dimers in the Gas Phase and in an Aqueous Solution , 1996 .

[149]  M Karplus,et al.  Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations. , 1998, Journal of molecular biology.

[150]  Michael R. Shirts,et al.  Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. , 2005, The Journal of chemical physics.

[151]  B. Roux,et al.  Energetics of ion conduction through the K + channel , 2022 .

[152]  Gregory A Voth,et al.  Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[153]  C. Brooks,et al.  Constant‐pH molecular dynamics using continuous titration coordinates , 2004, Proteins.

[154]  P. Kollman,et al.  Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation , 1993 .

[155]  Peter G Schultz,et al.  Adding amino acids to the genetic repertoire. , 2005, Current opinion in chemical biology.

[156]  D. Chandler,et al.  Theory of the hydrophobic effect , 1977 .

[157]  A. Horovitz,et al.  Double-mutant cycles: a powerful tool for analyzing protein structure and function. , 1996, Folding & design.

[158]  William L. Jorgensen,et al.  Relative partition coefficients for organic solutes from fluid simulations , 1990 .

[159]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[160]  A. Pohorille,et al.  Concentrations of anesthetics across the water-membrane interface; the Meyer-Overton hypothesis revisited. , 1998, Toxicology letters.

[161]  M. Karplus,et al.  On the Treatment of Electrostatic Interactions in Biomolecular Simulations , 1991 .

[162]  A T Brünger,et al.  Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations. , 1992, Biochemistry.

[163]  Lu Wang,et al.  Inclusion of Loss of Translational and Rotational Freedom in Theoretical Estimates of Free Energies of Binding. Application to a Complex of Benzene and Mutant T4 Lysozyme , 1997 .

[164]  M. Klein,et al.  Distribution of halothane in a dipalmitoylphosphatidylcholine bilayer from molecular dynamics calculations. , 2000, Biophysical journal.

[165]  A. Warshel,et al.  Dispersed polaron simulations of electron transfer in photosynthetic reaction centers. , 1989, Science.

[166]  S J Wodak,et al.  Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[167]  M Karplus,et al.  The meaning of component analysis: decomposition of the free energy in terms of specific interactions. , 1995, Journal of molecular biology.

[168]  U. Singh,et al.  Hydrophobic hydration: A free energy perturbation study , 1989 .

[169]  A. Warshel,et al.  Energetics of enzyme catalysis. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[170]  J. A. McCammon,et al.  Solvation structure of a sodium chloride ion pair in water , 1986 .

[171]  F. J. Luque,et al.  Theoretical determination of the solvation free energy in water and chloroform of the nucleic acid bases , 1996 .

[172]  Andrew Pohorille,et al.  Hydrophobic effects and modeling of biophysical aqueous solution interfaces. , 2002, Chemical reviews.

[173]  Michael R. Shirts,et al.  Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins , 2003 .

[174]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .

[175]  Thomas Simonson,et al.  Electrostatics and dynamics of proteins , 2003 .

[176]  K. Schulten,et al.  Molecular dynamics study of unbinding of the avidin-biotin complex. , 1997, Biophysical journal.

[177]  Irwin D Kuntz,et al.  Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. , 2003, Biopolymers.

[178]  B. Berne,et al.  Molecular Dynamics Calculation of the Effect of Solvent Polarizability on the Hydrophobic Interaction , 1995 .

[179]  Lars Ridder,et al.  Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide. , 2002, Journal of the American Chemical Society.

[180]  B. Roux,et al.  Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands , 2004, Nature.

[181]  Wilfred F van Gunsteren,et al.  Free energies of ligand binding for structurally diverse compounds. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[182]  John Bohannon.  Grassroots Supercomputing , 2005, Science.

[183]  B. Berne,et al.  The free energy landscape for β hairpin folding in explicit water , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[184]  Benoît Roux,et al.  Electrostatic free energy calculations using the generalized solvent boundary potential method , 2002 .

[185]  William L. Jorgensen,et al.  Do denaturants interact with aromatic hydrocarbons in water , 1993 .

[186]  Wilfred F. van Gunsteren,et al.  The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers. , 2001 .

[187]  James Andrew McCammon,et al.  Ligand-receptor interactions , 1984, Comput. Chem..

[188]  H. Resat,et al.  FREE ENERGY SIMULATIONS : CORRECTING FOR ELECTROSTATIC CUTOFFS BY USE OF THE POISSON EQUATION , 1996 .

[189]  M S Sansom,et al.  Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces. , 2001, Biophysical journal.

[190]  P A Kollman,et al.  Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches , 1993, Proteins.

[191]  Wilfred F van Gunsteren,et al.  Calculation of the Redox Potential of the Protein Azurin and Some Mutants , 2005, Chembiochem : a European journal of chemical biology.

[192]  Jens Carlsson,et al.  Absolute and relative entropies from computer simulation with applications to ligand binding. , 2005, The journal of physical chemistry. B.

[193]  Benoît Roux,et al.  Ion conduction and selectivity in K(+) channels. , 2005, Annual review of biophysics and biomolecular structure.