Alchemical free energy methods for drug discovery: progress and challenges.
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David L Mobley | Kim Branson | Michael R Shirts | Michael R. Shirts | Vijay S Pande | John D Chodera | Richard W Dixon | D. Mobley | M. Shirts | V. Pande | J. Chodera | R. Dixon | K. Branson
[1] R M Stroud,et al. Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate. , 1990, Biochemistry.
[2] Edmond Chow,et al. Desmond Performance on a Cluster of Multicore Processors , 2008 .
[3] B. Roux,et al. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. , 2006, Biophysical journal.
[4] R. Levy,et al. Simulating replica exchange simulations of protein folding with a kinetic network model , 2007, Proceedings of the National Academy of Sciences.
[5] E. Maginn,et al. Computing the melting point and thermodynamic stability of the orthorhombic and monoclinic crystalline polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride. , 2007, The Journal of chemical physics.
[6] Emilio Gallicchio,et al. The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. , 2010, Journal of chemical theory and computation.
[7] K. Sanbonmatsu,et al. α-Helical stabilization by side chain shielding of backbone hydrogen bonds , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[8] 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.
[9] Thomas Steinbrecher,et al. A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase. , 2006, Journal of medicinal chemistry.
[10] Thomas Steinbrecher,et al. Bornyl (3,4,5-trihydroxy)-cinnamate--an optimized human neutrophil elastase inhibitor designed by free energy calculations. , 2008, Bioorganic & medicinal chemistry.
[11] David L Mobley,et al. Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. , 2007, The Journal of chemical physics.
[12] Michael R. Shirts,et al. Statistically optimal analysis of samples from multiple equilibrium states. , 2008, The Journal of chemical physics.
[13] Takashi Amisaki,et al. Development of MD Engine: High‐speed accelerator with parallel processor design for molecular dynamics simulations , 1999 .
[14] Gisbert Schneider,et al. Virtual screening: an endless staircase? , 2010, Nature Reviews Drug Discovery.
[15] Kenneth M. Merz,et al. Free Energy Perturbation Study of Octanol/Water Partition Coefficients: Comparison with Continuum GB/SA Calculations , 1999 .
[16] J. Essex,et al. Hit identification and binding mode predictions by rigorous free energy simulations. , 2008, Journal of medicinal chemistry.
[17] Vijay S Pande,et al. Enhanced modeling via network theory: Adaptive sampling of Markov state models. , 2010, Journal of chemical theory and computation.
[18] Scott P. Brown,et al. Healthy skepticism: assessing realistic model performance. , 2009, Drug discovery today.
[19] Robert V. Swift,et al. Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics , 2009, J. Comput. Chem..
[20] David E. Shaw,et al. A fast, scalable method for the parallel evaluation of distance‐limited pairwise particle interactions , 2005, J. Comput. Chem..
[21] J. Guthrie,et al. A blind challenge for computational solvation free energies: introduction and overview. , 2009, The journal of physical chemistry. B.
[22] H. Stern. Molecular simulation with variable protonation states at constant pH. , 2007, The Journal of chemical physics.
[23] G. Norris. Boeing's seventh wonder , 1995 .
[24] Jonathan Greer,et al. Influenza neuraminidase inhibitors: structure-based design of a novel inhibitor series. , 2003, Biochemistry.
[25] Gerhard Klebe,et al. Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments. , 2007, Journal of molecular biology.
[26] 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.
[27] James Andrew McCammon,et al. Ligand-receptor interactions , 1984, Comput. Chem..
[28] Christophe Chipot,et al. Good practices in free-energy calculations. , 2010, The journal of physical chemistry. B.
[29] Guohui Li,et al. Trypsin‐ligand binding free energies from explicit and implicit solvent simulations with polarizable potential , 2009, J. Comput. Chem..
[30] P. Kollman,et al. Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.
[31] 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.
[32] Fredrik Edfeldt,et al. Affinity-based, biophysical methods to detect and analyze ligand binding to recombinant proteins: matching high information content with high throughput. , 2010, Journal of structural biology.
[33] Michael R Shirts,et al. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. , 2006, The Journal of chemical physics.
[34] K. Dill,et al. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". , 2009, Structure.
[35] Thomas Simonson,et al. Alchemical free energy simulations for biological complexes: powerful but temperamental … , 2009, Journal of molecular recognition : JMR.
[36] Themis Lazaridis,et al. Contributions to the binding free energy of ligands to avidin and streptavidin , 2002, Proteins.
[37] M. Rami Reddy,et al. Free energy calculations in rational drug design , 2001 .
[38] Benoît Roux,et al. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. , 2010, Journal of chemical theory and computation.
[39] C. Vega,et al. Solubility of KF and NaCl in water by molecular simulation. , 2007, The Journal of chemical physics.
[40] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[41] Vijay S. Pande,et al. Everything you wanted to know about Markov State Models but were afraid to ask. , 2010, Methods.
[42] William L. Jorgensen,et al. Eastern extension of azoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase; cyano group alternatives. , 2010, Bioorganic & medicinal chemistry letters.
[43] R. Dror,et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.
[44] 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 .
[45] M J Harvey,et al. ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. , 2009, Journal of chemical theory and computation.
[46] B. Roux,et al. Computations of standard binding free energies with molecular dynamics simulations. , 2009, The journal of physical chemistry. B.
[47] Wei Yang,et al. Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence. , 2004, The Journal of chemical physics.
[48] 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.
[49] David L Mobley,et al. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. , 2009, Journal of molecular biology.
[50] V. Pande,et al. Rapid equilibrium sampling initiated from nonequilibrium data , 2009, Proceedings of the National Academy of Sciences.
[51] K. Dill,et al. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. , 2006, The Journal of chemical physics.
[52] Nobuaki Miyakawa,et al. Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations , 1999, J. Comput. Chem..
[53] Vijay S. Pande,et al. Accelerating molecular dynamic simulation on graphics processing units , 2009, J. Comput. Chem..
[54] B Honig,et al. Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. , 1991, Biochemistry.
[55] David L Mobley,et al. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. , 2008, Journal of medicinal chemistry.
[56] Eric J. Sorin,et al. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. , 2005, Biophysical journal.
[57] Thomas Simonson,et al. Protonation Patterns in Tetracycline:Tet Repressor Recognition: Simulations and Experiments , 2007, Chembiochem : a European journal of chemical biology.
[58] Julien Michel,et al. Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization? , 2006, Journal of medicinal chemistry.
[59] Mika A. Kastenholz,et al. Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids. , 2006, The Journal of chemical physics.
[60] Wilfred F van Gunsteren,et al. Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation , 2003, Proteins.
[61] Benoît Roux,et al. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations. , 2008, The Journal of chemical physics.
[62] Benoît Roux,et al. Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD). , 2009, Journal of chemical theory and computation.
[63] David L. Mobley,et al. Drug Design: Free-energy calculations in structure-based drug design , 2010 .
[64] John Mongan,et al. Biomolecular simulations at constant pH. , 2005, Current opinion in structural biology.
[65] Anthony Nicholls,et al. SAMPL2 challenge: prediction of solvation energies and tautomer ratios , 2010, J. Comput. Aided Mol. Des..
[66] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[67] Hans W. Horn,et al. Accounting for polarization cost when using fixed charge force fields. II. Method and application for computing effect of polarization cost on free energy of hydration. , 2010, The journal of physical chemistry. B.
[68] R. Stroud,et al. Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate. , 1990 .
[69] B. Shoichet,et al. Decoys for docking. , 2005, Journal of medicinal chemistry.
[70] Pengyu Y. Ren,et al. Calculation of protein–ligand binding free energy by using a polarizable potential , 2008, Proceedings of the National Academy of Sciences.
[71] Wilfred F. van Gunsteren,et al. Basic ingredients of free energy calculations: A review , 2009, J. Comput. Chem..
[72] Charles L. Brooks,et al. Efficient Sampling of Ligand Orientations and Conformations in Free Energy Calculations Using the λ-Dynamics Method , 2000 .
[73] William L Jorgensen,et al. Efficient drug lead discovery and optimization. , 2009, Accounts of chemical research.
[74] Alexander D. MacKerell,et al. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. , 2010, Journal of chemical theory and computation.
[75] Charles C. Persinger,et al. How to improve R&D productivity: the pharmaceutical industry's grand challenge , 2010, Nature Reviews Drug Discovery.
[76] Vijay S. Pande,et al. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit , 2010, J. Comput. Chem..
[77] Matthew Clark,et al. Grand Canonical Monte Carlo Simulation of Ligand-Protein Binding , 2006, J. Chem. Inf. Model..
[78] Benoît Roux,et al. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl‐transferase P‐site using molecular dynamics simulations with restraining potentials , 2010, Journal of molecular recognition : JMR.
[79] Julian Tirado-Rives,et al. Vancomycin resistance: modeling backbone variants with D-Ala-D-Ala and D-Ala-D-Lac peptides. , 2009, Bioorganic & medicinal chemistry letters.
[80] David L. Mobley,et al. Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations , 2010, J. Comput. Aided Mol. Des..
[81] Wei Yang,et al. Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems , 2008, Proceedings of the National Academy of Sciences.
[82] Wayne Vaccaro,et al. Multiple and single binding modes of fragment-like kinase inhibitors revealed by molecular modeling, residue type-selective protonation, and nuclear overhauser effects. , 2008, Journal of medicinal chemistry.
[83] Mika A. Kastenholz,et al. Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation. , 2006, The Journal of chemical physics.
[84] V. Pande,et al. Error analysis and efficient sampling in Markovian state models for molecular dynamics. , 2005, The Journal of chemical physics.
[85] B. Roux,et al. Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome. , 2010, The journal of physical chemistry. B.
[86] Margaret E. Johnson,et al. Current status of the AMOEBA polarizable force field. , 2010, The journal of physical chemistry. B.
[87] David L Mobley,et al. The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. , 2007, Journal of chemical theory and computation.
[88] Emilio Gallicchio,et al. Advances in all atom sampling methods for modeling protein-ligand binding affinities. , 2011, Current opinion in structural biology.
[89] Thomas S. Peat,et al. Practical Aspects of the SAMPL Challenge: Providing an Extensive Experimental Data Set for the Modeling Community , 2009, Journal of biomolecular screening.
[90] David L Mobley,et al. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. , 2009, Journal of chemical theory and computation.
[91] Andrew S. Paluch,et al. A method for computing the solubility limit of solids: application to sodium chloride in water and alcohols. , 2010, The Journal of chemical physics.
[92] Jonathan W. Essex,et al. Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations , 2010, J. Comput. Aided Mol. Des..
[93] F Marty Ytreberg. Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations. , 2009, The Journal of chemical physics.
[94] H. Fujitani,et al. Massively parallel computation of absolute binding free energy with well-equilibrated states. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.
[95] Yvonne C. Martin,et al. Let’s not forget tautomers , 2009, J. Comput. Aided Mol. Des..
[96] William L. Jorgensen,et al. Optimization of azoles as anti-human immunodeficiency virus agents guided by free-energy calculations. , 2008, Journal of the American Chemical Society.
[97] Ron O. Dror,et al. Publisher's Note: Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations [Phys. Rev. E80, 046705 (2009)] , 2009 .
[98] K. Dill,et al. Predicting absolute ligand binding free energies to a simple model site. , 2007, Journal of molecular biology.
[99] Benoît Roux,et al. Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant. , 2006, Journal of chemical theory and computation.
[100] V. Pande,et al. Multiplexed-replica exchange molecular dynamics method for protein folding simulation. , 2003, Biophysical journal.
[101] R. Duggleby,et al. Determination of inhibition constants, I50 values and the type of inhibition for enzyme-catalyzed reactions. , 1988, Biochemical medicine and metabolic biology.
[102] Sergei Yu Noskov,et al. Evaluations of the Absolute and Relative Free Energies for Antidepressant Binding to the Amino Acid Membrane Transporter LeuT with Free Energy Simulations. , 2010, Journal of chemical theory and computation.
[103] D. Case,et al. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. , 2008, Journal of molecular biology.
[104] 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..
[105] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[106] Miguel Jorge,et al. 1-Octanol/Water Partition Coefficients of n-Alkanes from Molecular Simulations of Absolute Solvation Free Energies. , 2009, Journal of chemical theory and computation.
[107] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[108] G. Hummer,et al. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. , 2009, The journal of physical chemistry. B.
[109] David E. Shaw,et al. Zonal methods for the parallel execution of range-limited N-body simulations , 2007, J. Comput. Phys..
[110] Wei Yang,et al. Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations. , 2007, The Journal of chemical physics.
[111] Klaus Schulten,et al. GPU-accelerated molecular modeling coming of age. , 2010, Journal of molecular graphics & modelling.
[112] David L Mobley,et al. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. , 2007, The journal of physical chemistry. B.