Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions
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[1] J. Irwin,et al. Lead discovery using molecular docking. , 2002, Current opinion in chemical biology.
[2] E. M.,et al. Statistical Mechanics , 2021, Manual for Theoretical Chemistry.
[3] G. Klebe,et al. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. , 2005, Journal of medicinal chemistry.
[4] Hans-Joachim Böhm,et al. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..
[5] I. Kuntz,et al. Automated docking with grid‐based energy evaluation , 1992 .
[6] R Nussinov,et al. A set of van der Waals and coulombic radii of protein atoms for molecular and solvent‐accessible surface calculation, packing evaluation, and docking , 1998, Proteins.
[7] Ajay,et al. Computational methods to predict binding free energy in ligand-receptor complexes. , 1995, Journal of medicinal chemistry.
[8] Janet M. Thornton,et al. BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential , 1999 .
[9] A. Davis,et al. Hydrogen Bonding, Hydrophobic Interactions, and Failure of the Rigid Receptor Hypothesis. , 1999, Angewandte Chemie.
[10] Janet M. Thornton,et al. BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential , 1999, J. Comput. Chem..
[11] Renxiao Wang,et al. The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. , 2004, Journal of medicinal chemistry.
[12] C. Brooks,et al. Recent advances in the development and application of implicit solvent models in biomolecule simulations. , 2004, Current opinion in structural biology.
[13] Xiaoqin Zou,et al. Efficient molecular docking of NMR structures: Application to HIV‐1 protease , 2006, Protein science : a publication of the Protein Society.
[14] Bernard Malissen,et al. Crystal structure of a T cell receptor bound to an allogeneic MHC molecule , 2000, Nature Immunology.
[15] I. Kuntz,et al. Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model , 1999 .
[16] Luhua Lai,et al. Further development and validation of empirical scoring functions for structure-based binding affinity prediction , 2002, J. Comput. Aided Mol. Des..
[17] ANATOLY M. RUVINSKY. Role of binding entropy in the refinement of protein–ligand docking predictions: Analysis based on the use of 11 scoring functions , 2007, J. Comput. Chem..
[18] David S. Goodsell,et al. Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes , 2008, J. Comput. Chem..
[19] X. Zou,et al. Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking , 2006, Proteins.
[20] M. Gilson,et al. Ligand configurational entropy and protein binding , 2007, Proceedings of the National Academy of Sciences.
[21] Todd J. A. Ewing,et al. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases , 2001, J. Comput. Aided Mol. Des..
[22] Song Liu,et al. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. , 2005, Journal of medicinal chemistry.
[23] Thomas Lengauer,et al. A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.
[24] M. Gilson,et al. The statistical-thermodynamic basis for computation of binding affinities: a critical review. , 1997, Biophysical journal.
[25] M. Sippl. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.
[26] Anatoly M. Ruvinsky,et al. Calculations of protein-ligand binding entropy of relative and overall molecular motions , 2007, J. Comput. Aided Mol. Des..
[27] Hans-Joachim Böhm,et al. Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs , 1998, J. Comput. Aided Mol. Des..
[28] Xiaojie Xu,et al. Empirical Aqueous Solvation Models Based on Accessible Surface Areas with Implicit Electrostatics , 2002 .
[29] M R Lee,et al. Use of MM‐PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece , 2000, Proteins.
[30] 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.
[31] G. V. Paolini,et al. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes , 1997, J. Comput. Aided Mol. Des..
[32] I. Muegge. PMF scoring revisited. , 2006, Journal of medicinal chemistry.
[33] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[34] P. Kollman,et al. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. , 2001, Annual review of biophysics and biomolecular structure.
[35] K. Dill,et al. An iterative method for extracting energy-like quantities from protein structures. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[36] M. V. Subbotin,et al. PLASS: Protein-ligand affinity statistical score – a knowledge-based force-field model of interaction derived from the PDB , 2004, J. Comput. Aided Mol. Des..
[37] Janet M. Thornton,et al. Evaluation of a knowledge‐based potential of mean force for scoring docked protein–ligand complexes , 2001, J. Comput. Chem..
[38] Conrad C. Huang,et al. UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..
[39] E. Lomba,et al. Determination of the interaction potential from the pair distribution function: an inverse Monte Carlo technique. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[40] Martin Stahl,et al. The Use of Scoring Functions in Drug Discovery Applications , 2003 .
[41] Abby L. Parrill,et al. Rational drug design : novel methodology and practical applications , 1999 .
[42] Renxiao Wang,et al. Comparative evaluation of 11 scoring functions for molecular docking. , 2003, Journal of medicinal chemistry.
[43] P. Kollman,et al. An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.
[44] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[45] Gennady M Verkhivker,et al. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. , 1995, Chemistry & biology.
[46] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[47] Shaomeng Wang,et al. M-score: a knowledge-based potential scoring function accounting for protein atom mobility. , 2006, Journal of medicinal chemistry.
[48] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[49] E. Shakhnovich,et al. SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence , 1996 .
[50] Marcel L Verdonk,et al. General and targeted statistical potentials for protein–ligand interactions , 2005, Proteins.
[51] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..
[52] Y. Martin,et al. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. , 1999, Journal of medicinal chemistry.
[53] K. Dill,et al. Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.
[54] E. Shakhnovich,et al. SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. , 2002, Journal of medicinal chemistry.
[55] Ajay N. Jain. Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities , 1996, J. Comput. Aided Mol. Des..
[56] SHENG-YOU HUANG,et al. An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials , 2006, J. Comput. Chem..
[57] G. Klebe,et al. Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.
[58] I. Kuntz,et al. Pairwise GB/SA Scoring Function for Structure-based Drug Design , 2004 .
[59] H. Scheraga,et al. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. , 1976, Macromolecules.
[60] Nathan A. Baker,et al. Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[61] William H. Press,et al. Numerical recipes in Fortran 77 : the art of scientificcomputing. , 1992 .
[62] R L Jernigan,et al. A preference‐based free‐energy parameterization of enzyme‐inhibitor binding. Applications to HIV‐1‐protease inhibitor design , 1995, Protein science : a publication of the Protein Society.
[63] J. Andrew Grant,et al. A smooth permittivity function for Poisson–Boltzmann solvation methods , 2001, J. Comput. Chem..
[64] M. Sippl. Calculation of conformational ensembles from potentials of mena force , 1990 .
[65] R. Harrison,et al. Prediction of new serine proteinase inhibitors , 1994, Nature Structural Biology.
[66] Emil Alexov,et al. Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects , 2002, J. Comput. Chem..
[67] Garland R. Marshall,et al. VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands , 1996 .
[68] U. Singh,et al. A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .
[69] A V Finkelstein,et al. The price of lost freedom: entropy of bimolecular complex formation. , 1989, Protein engineering.
[70] Xiaoqin Zou,et al. An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function , 2006, J. Comput. Chem..
[71] Luhua Lai,et al. Estimating protein–ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation , 2004, Proteins.
[72] W A Koppensteiner,et al. Knowledge-based potentials--back to the roots. , 1998, Biochemistry. Biokhimiia.
[73] Natasja Brooijmans,et al. Molecular recognition and docking algorithms. , 2003, Annual review of biophysics and biomolecular structure.
[74] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[75] B. Matthews,et al. A model binding site for testing scoring functions in molecular docking. , 2002, Journal of molecular biology.
[76] Renxiao Wang,et al. The PDBbind database: methodologies and updates. , 2005, Journal of medicinal chemistry.
[77] P. Kollman,et al. Solvation Model Based on Weighted Solvent Accessible Surface Area , 2001 .
[78] M. Rami Reddy,et al. Free energy calculations in rational drug design , 2001 .
[79] Gerhard Klebe,et al. Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function , 2000 .
[80] Gennady M Verkhivker,et al. Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. , 1995, Protein engineering.
[81] S Vajda,et al. Empirical potentials and functions for protein folding and binding. , 1997, Current opinion in structural biology.
[82] P A Kollman,et al. Continuum solvent studies of the stability of RNA hairpin loops and helices. , 1998, Journal of biomolecular structure & dynamics.
[83] David S. Goodsell,et al. A semiempirical free energy force field with charge‐based desolvation , 2007, J. Comput. Chem..
[84] U. Singh,et al. Development of a quantum mechanics-based free-energy perturbation method: use in the calculation of relative solvation free energies. , 2004, Journal of the American Chemical Society.
[85] Xiaoqin Zou,et al. Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach. , 2006, The journal of physical chemistry. B.
[86] Xiaoqin Zou,et al. An iterative knowledge‐based scoring function for protein–protein recognition , 2008, Proteins.