Accommodating protein flexibility for structure-based drug design.
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[1] Chung F Wong,et al. Flexible ligand-flexible protein docking in protein kinase systems. , 2008, Biochimica et biophysica acta.
[2] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .
[3] Thomas Lengauer,et al. Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking , 1999, Proteins.
[4] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[5] Stefan Janson,et al. Molecular docking with multi-objective Particle Swarm Optimization , 2008, Appl. Soft Comput..
[6] Jinn-Moon Yang,et al. GEMDOCK: A generic evolutionary method for molecular docking , 2004, Proteins.
[7] Shaomeng Wang,et al. An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes , 2004, J. Chem. Inf. Model..
[8] D. J. Price,et al. Assessing scoring functions for protein-ligand interactions. , 2004, Journal of medicinal chemistry.
[9] David E. Clark,et al. Evolutionary Algorithms in Molecular Design , 1999 .
[10] W Patrick Walters,et al. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance , 2004, Proteins.
[11] Roger J.-B. Wets,et al. Minimization by Random Search Techniques , 1981, Math. Oper. Res..
[12] Zhihai Liu,et al. Comparative Assessment of Scoring Functions on a Diverse Test Set , 2009, J. Chem. Inf. Model..
[13] J. Aqvist,et al. A new method for predicting binding affinity in computer-aided drug design. , 1994, Protein engineering.
[14] R. Glen,et al. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. , 1995, Journal of molecular biology.
[15] Peter L. Freddolino,et al. Force field bias in protein folding simulations. , 2009, Biophysical journal.
[16] Steven W. Muchmore,et al. Rapid Estimation of Relative Protein-Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA , 2007, J. Chem. Inf. Model..
[17] V. Sobolev,et al. Flexibility of metal binding sites in proteins on a database scale , 2005, Proteins.
[18] John H. Holland,et al. Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .
[19] Judith Herzfeld,et al. Functional and shunt states of bacteriorhodopsin resolved by 250 GHz dynamic nuclear polarization–enhanced solid-state NMR , 2009, Proceedings of the National Academy of Sciences.
[20] Shiow-Fen Hwang,et al. SODOCK: Swarm optimization for highly flexible protein–ligand docking , 2007, J. Comput. Chem..
[21] Jung-Hsin Lin,et al. Optimization and Computational Evaluation of a Series of Potential Active Site Inhibitors of the V82F/I84V Drug‐resistant Mutant of HIV‐1 Protease: an Application of the Relaxed Complex Method of Structure‐based Drug Design , 2006, Chemical biology & drug design.
[22] Julien Michel,et al. Prediction of the water content in protein binding sites. , 2009, The journal of physical chemistry. B.
[23] Osamu Miyashita,et al. Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose. , 2009, Biophysical journal.
[24] 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..
[25] M. Karplus,et al. Method for estimating the configurational entropy of macromolecules , 1981 .
[26] Steven W. Muchmore,et al. High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing , 2006, J. Chem. Inf. Model..
[27] Boguslaw Stec,et al. Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments , 2007, Proteins.
[28] Matthew P. Repasky,et al. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. , 2006, Journal of medicinal chemistry.
[29] P. Kollman,et al. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding , 2000 .
[30] P. Hajduk,et al. Discovering High-Affinity Ligands for Proteins: SAR by NMR , 1996, Science.
[31] Rommie E. Amaro,et al. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design , 2008, J. Comput. Aided Mol. Des..
[32] René Thomsen,et al. MolDock: a new technique for high-accuracy molecular docking. , 2006, Journal of medicinal chemistry.
[33] R Abagyan,et al. Flexible protein–ligand docking by global energy optimization in internal coordinates , 1997, Proteins.
[34] Luhua Lai,et al. Further development and validation of empirical scoring functions for structure-based binding affinity prediction , 2002, J. Comput. Aided Mol. Des..
[35] John Bradshaw,et al. Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms , 1998, J. Chem. Inf. Comput. Sci..
[36] R. Abagyan,et al. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. , 1994, Journal of molecular biology.
[37] M Karplus,et al. The contribution of cross‐links to protein stability: A normal mode analysis of the configurational entropy of the native state , 1993, Proteins.
[38] Rudolph A. Marcus,et al. Chemical and Electrochemical Electron-Transfer Theory , 1964 .
[39] J. Mccammon,et al. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. , 2002, Journal of the American Chemical Society.
[40] Alexandre M. J. J. Bonvin,et al. Solvated docking: introducing water into the modelling of biomolecular complexes , 2006, Bioinform..
[41] Jason C. Cole,et al. Testing Assumptions and Hypotheses for Rescoring Success in Protein-Ligand Docking , 2009, J. Chem. Inf. Model..
[42] Somesh D. Sharma,et al. Managing protein flexibility in docking and its applications. , 2009, Drug discovery today.
[43] Jung-Hsin Lin,et al. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. , 2003, Biopolymers.
[44] Yen-Jen Oyang,et al. MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm , 2005, Nucleic Acids Res..
[45] Stewart A. Adcock,et al. Molecular dynamics: survey of methods for simulating the activity of proteins. , 2006, Chemical reviews.
[46] Thomas M. Cover,et al. Elements of Information Theory , 2005 .