Molecular recognition and docking algorithms.
暂无分享,去创建一个
[1] Jonathan D. Hirst,et al. Assessing search strategies for flexible docking , 1998 .
[2] I D Kuntz,et al. Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D. , 1997, Chemistry & biology.
[3] Gennady Verkhivker,et al. Deciphering common failures in molecular docking of ligand-protein complexes , 2000, J. Comput. Aided Mol. Des..
[4] Yuan-Ping Pang,et al. EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases , 2001, J. Comput. Chem..
[5] M Rarey,et al. Detailed analysis of scoring functions for virtual screening. , 2001, Journal of medicinal chemistry.
[6] A. N. Jain,et al. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. , 1996, Chemistry & biology.
[7] Z. Xiang,et al. On the role of the crystal environment in determining protein side-chain conformations. , 2002, Journal of molecular biology.
[8] W. Kauzmann. Some factors in the interpretation of protein denaturation. , 1959, Advances in protein chemistry.
[9] P. Kollman,et al. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices , 1998 .
[10] M. Sternberg,et al. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. , 1998, Journal of molecular biology.
[11] 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.
[12] D J Diller,et al. High throughput docking for library design and library prioritization , 2001, Proteins.
[13] P. Goodford. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.
[14] F M Richards,et al. Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.
[15] John Marelius,et al. Calculation of Ligand Binding Free Energies from Molecular Dynamics Simulations , 1998 .
[16] F. Lombardo,et al. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , 1997 .
[17] I. Kuntz,et al. Ligand solvation in molecular docking , 1999, Proteins.
[18] Robert P. Sheridan,et al. FLOG: A system to select ‘quasi-flexible’ ligands complementary to a receptor of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..
[19] M L Lamb,et al. Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method. , 1998, Journal of medicinal chemistry.
[20] David E. Clark,et al. A comparison of heuristic search algorithms for molecular docking , 1997, J. Comput. Aided Mol. Des..
[21] Yvonne C. Martin,et al. Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection , 1996, J. Chem. Inf. Comput. Sci..
[22] John Bradshaw,et al. The Effectiveness of Reactant Pools for Generating Structurally-Diverse Combinatorial Libraries , 1997, J. Chem. Inf. Comput. Sci..
[23] Christopher W. Murray,et al. The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase , 1999, J. Comput. Aided Mol. Des..
[24] Johan Åqvist,et al. Ligand binding affinity prediction by linear interaction energy methods , 1998, J. Comput. Aided Mol. Des..
[25] M. Sternberg,et al. Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.
[26] Ruth Nussinov,et al. Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.
[27] Michael K. Gilson,et al. ''Mining minima'': Direct computation of conformational free energy , 1997 .
[28] D. Case,et al. Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.
[29] J. Mccammon,et al. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. , 2002, Journal of the American Chemical Society.
[30] E. Shakhnovich,et al. Analysis of knowledge‐based protein‐ligand potentials using a self‐consistent method , 2008, Protein science : a publication of the Protein Society.
[31] E. Shakhnovich,et al. SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. , 2002, Journal of medicinal chemistry.
[32] Ruhong Zhou,et al. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model , 1999 .
[33] W. L. Jorgensen,et al. Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density , 1998 .
[34] Michael W. Mahoney,et al. Diffusion constant of the TIP5P model of liquid water , 2001 .
[35] Thomas Lengauer,et al. Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking , 1999, Proteins.
[36] I. Kuntz,et al. Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model , 1999 .
[37] S. Kim,et al. "Soft docking": matching of molecular surface cubes. , 1991, Journal of molecular biology.
[38] Gerhard Klebe,et al. Recent developments in structure-based drug design , 2000, Journal of Molecular Medicine.
[39] Malin M. Young,et al. Design, docking, and evaluation of multiple libraries against multiple targets , 2001, Proteins.
[40] Andreas Plückthun,et al. Docking small ligands in flexible binding sites , 1998 .
[41] 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..
[42] I. Kuntz,et al. Conformational analysis of flexible ligands in macromolecular receptor sites , 1992 .
[43] Janet M. Thornton,et al. BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential , 1999, J. Comput. Chem..
[44] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .
[45] B. Shoichet,et al. Flexible ligand docking using conformational ensembles , 1998, Protein science : a publication of the Protein Society.
[46] David A. Case,et al. Effective Born radii in the generalized Born approximation: The importance of being perfect , 2002, J. Comput. Chem..
[47] Thomas Lengauer,et al. A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.
[48] M J Sternberg,et al. Empirical scale of side-chain conformational entropy in protein folding. , 1993, Journal of molecular biology.
[49] M. Murcko,et al. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. , 1999, Journal of medicinal chemistry.
[50] Mark A. Murcko,et al. Virtual screening : an overview , 1998 .
[51] D. Koshland. Application of a Theory of Enzyme Specificity to Protein Synthesis. , 1958, Proceedings of the National Academy of Sciences of the United States of America.
[52] I. Kuntz,et al. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. , 1988, Journal of medicinal chemistry.
[53] P. Kollman,et al. Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation , 2002, Proteins.
[54] B. Bush,et al. Macromolecular shape and surface maps by solvent exclusion. , 1978, Proceedings of the National Academy of Sciences of the United States of America.
[55] D. Goodsell,et al. Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock , 2002, Proteins.
[56] R M Knegtel,et al. Efficacy and selectivity in flexible database docking , 1999, Proteins.
[57] R. Abagyan,et al. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. , 1994, Journal of molecular biology.
[58] J. Scott Dixon,et al. Flexible ligand docking using a genetic algorithm , 1995, J. Comput. Aided Mol. Des..
[59] I. Kuntz,et al. Flexible ligand docking: A multistep strategy approach , 1999, Proteins.
[60] E. Freire,et al. Direct measurement of protein binding energetics by isothermal titration calorimetry. , 2001, Current opinion in structural biology.
[61] L. Pauling,et al. THE NATURE OF THE INTERMOLECULAR FORCES OPERATIVE IN BIOLOGICAL PROCESSES. , 1940, Science.
[62] Fenglou Mao,et al. Potential of mean force for protein–protein interaction studies , 2002, Proteins.
[63] T. L. Blundell,et al. DOCKER, an interactive program for simulating protein receptor and substrate interactions , 1983 .
[64] I D Kuntz,et al. Inhibitors of kinesin activity from structure-based computer screening. , 2000, Biochemistry.
[65] Janet M. Thornton,et al. BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential , 1999 .
[66] I. Kuntz,et al. Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[67] Peter A. Kollman,et al. Computational alanine scanning of the 1:1 human growth hormone–receptor complex , 2002, J. Comput. Chem..
[68] C. Lipinski. Drug-like properties and the causes of poor solubility and poor permeability. , 2000, Journal of pharmacological and toxicological methods.
[69] Richard S. Judson,et al. Docking flexible molecules: A case study of three proteins , 1995, J. Comput. Chem..
[70] 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..
[71] M. L. Connolly. Analytical molecular surface calculation , 1983 .
[72] A. Kidera,et al. Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides , 1997 .
[73] S. Wodak,et al. Hemoglobin interaction in sickle cell fibers. I: Theoretical approaches to the molecular contacts. , 1975, Proceedings of the National Academy of Sciences of the United States of America.
[74] E. Alexov,et al. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. , 2002, Biophysical journal.
[75] F R Salemme,et al. An hypothetical structure for an intermolecular electron transfer complex of cytochromes c and b5. , 1976, Journal of molecular biology.
[76] Nobuo Tomioka,et al. A method for fast energy estimation and visualization of protein-ligand interaction , 1987, J. Comput. Aided Mol. Des..
[77] E. Fischer. Einfluss der Configuration auf die Wirkung der Enzyme , 1894 .
[78] I. Kuntz,et al. Molecular docking to ensembles of protein structures. , 1997, Journal of molecular biology.
[79] H A Scheraga,et al. Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[80] Yvonne C. Martin,et al. The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding , 1997, J. Chem. Inf. Comput. Sci..
[81] A Caflisch,et al. Monte Carlo docking of oligopeptides to proteins , 1992, Proteins.
[82] Marvin Waldman,et al. Evaluation of Reagent-Based and Product-Based Strategies in the Design of Combinatorial Library Subsets , 2000, J. Chem. Inf. Comput. Sci..
[83] Youngshang Pak,et al. Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems , 2000 .
[84] P. Kollman,et al. Solvation Model Based on Weighted Solvent Accessible Surface Area , 2001 .
[85] J. Åqvist,et al. Calculation of absolute binding free energies for charged ligands and effects of long‐range electrostatic interactions , 1996 .
[86] Rebecca C. Wade,et al. COMPUTATIONAL ALCHEMY TO CALCULATE ABSOLUTE PROTEIN-LIGAND BINDING FREE ENERGY , 1998 .
[87] G. Klebe,et al. Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.
[88] Haruki Nakamura,et al. Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation , 1997 .
[89] Paul S. Charifson,et al. Practical Application of Computer-Aided Drug Design , 1997 .
[90] D. Rognan,et al. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. , 2000, Journal of medicinal chemistry.
[91] V. Pande,et al. Absolute comparison of simulated and experimental protein-folding dynamics , 2002, Nature.
[92] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[93] Tudor I. Oprea. Current trends in lead discovery: Are we looking for the appropriate properties? , 2002, J. Comput. Aided Mol. Des..
[94] R. Clark,et al. Consensus scoring for ligand/protein interactions. , 2002, Journal of molecular graphics & modelling.
[95] Charles L. Brooks,et al. Assessing energy functions for flexible docking , 1998 .
[96] Heather A. Carlson,et al. Free energies of solvation in chloroform and water from a linear response approach , 1997 .
[97] Alexander A. Rashin,et al. Hydration phenomena, classical electrostatics, and the boundary element method , 1990 .
[98] H. Scheraga,et al. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[99] Ingo Muegge,et al. Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors , 2000, J. Comput. Aided Mol. Des..
[100] A Aitken,et al. Expression and structural analysis of 14-3-3 proteins. , 1995, Journal of molecular biology.
[101] E. Shakhnovich,et al. SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence , 1996 .
[102] Shaomeng Wang,et al. MCDOCK: A Monte Carlo simulation approach to the molecular docking problem , 1999, J. Comput. Aided Mol. Des..
[103] Y. Martin,et al. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. , 1999, Journal of medicinal chemistry.
[104] I D Kuntz,et al. Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: irreversible inhibition of infectivity , 1997, Journal of virology.
[105] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[106] Ruben Abagyan,et al. ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation , 1994, J. Comput. Chem..
[107] J. Aqvist,et al. A new method for predicting binding affinity in computer-aided drug design. , 1994, Protein engineering.
[108] R. Glen,et al. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. , 1995, Journal of molecular biology.
[109] H. Wolfson,et al. Shape complementarity at protein–protein interfaces , 1994, Biopolymers.
[110] H J Berendsen,et al. Molecular dynamics simulation of the docking of substrates to proteins , 1994, Proteins.
[111] William L. Jorgensen,et al. Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with Sustiva through Computation of Resistance Profiles , 2000 .
[112] Bin Xia,et al. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water , 2002, Journal of biomolecular NMR.
[113] S Vajda,et al. Prediction of protein complexes using empirical free energy functions , 1996, Protein science : a publication of the Protein Society.
[114] Thomas E. Ferrin,et al. Computer graphics in real‐time docking with energy calculation and minimization , 1985 .
[115] P. Kollman,et al. Investigating the binding specificity of U1A-RNA by computational mutagenesis. , 2000, Journal of molecular biology.
[116] 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.
[117] Thomas Lengauer,et al. FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.
[118] R Abagyan,et al. Flexible protein–ligand docking by global energy optimization in internal coordinates , 1997, Proteins.
[119] P. Kollman,et al. Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies , 1999 .
[120] A. di Nola,et al. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation , 1999, Proteins.
[121] Robert P. Sheridan,et al. Flexibases: A way to enhance the use of molecular docking methods , 1994, J. Comput. Aided Mol. Des..
[122] Thomas Lengauer,et al. Placement of medium-sized molecular fragments into active sites of proteins , 1996, J. Comput. Aided Mol. Des..
[123] 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..
[124] Donald G. Truhlar,et al. MODEL FOR AQUEOUS SOLVATION BASED ON CLASS IV ATOMIC CHARGES AND FIRST SOLVATION SHELL EFFECTS , 1996 .
[125] I. Kuntz,et al. Automated docking with grid‐based energy evaluation , 1992 .
[126] Y. Martin,et al. Do structurally similar molecules have similar biological activity? , 2002, Journal of medicinal chemistry.
[127] C. Milstein,et al. Conformational isomerism and the diversity of antibodies. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[128] J. Janin,et al. Computer studies of interactions between macromolecules. , 1987, Progress in biophysics and molecular biology.
[129] D. Goodsell,et al. Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.
[130] Peter A. Kollman,et al. A Ligand That Is Predicted to Bind Better to Avidin than Biotin: Insights from Computational Fluorine Scanning , 2000 .
[131] M. Karplus,et al. Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP—substrate complex , 1997 .
[132] P. Kollman,et al. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. , 2001, Journal of the American Chemical Society.
[133] A. Leach,et al. Ligand docking to proteins with discrete side-chain flexibility. , 1994, Journal of molecular biology.
[134] Piotr Cieplak,et al. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. , 2002, Journal of medicinal chemistry.
[135] Harold A. Scheraga,et al. Prodock: Software package for protein modeling and docking , 1999 .
[136] J. Janin,et al. Computer analysis of protein-protein interaction. , 1978, Journal of molecular biology.
[137] I. Kuntz,et al. Docking flexible ligands to macromolecular receptors by molecular shape. , 1986, Journal of medicinal chemistry.
[138] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.
[139] B. Honig,et al. A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation , 1991 .
[140] Ruhong Zhou,et al. New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model , 2001 .
[141] F. Allen. The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.
[142] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[143] Jan Hermans,et al. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model , 1998, Proteins.
[144] Gennady M Verkhivker,et al. Predicting structural effects in HIV‐1 protease mutant complexes with flexible ligand docking and protein side‐chain optimization , 1998, Proteins.
[145] P. Kollman,et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.