GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein-Ligand Complexes
暂无分享,去创建一个
[1] D. E. Clark,et al. Flexible docking using tabu search and an empirical estimate of binding affinity , 1998, Proteins.
[2] Adrian H Elcock,et al. Progress toward virtual screening for drug side effects , 2002, Proteins.
[3] Paul N. Mortenson,et al. Diverse, high-quality test set for the validation of protein-ligand docking performance. , 2007, Journal of medicinal chemistry.
[4] C. E. Peishoff,et al. A critical assessment of docking programs and scoring functions. , 2006, Journal of medicinal chemistry.
[5] Joannis Apostolakis,et al. Graph-Based Molecular Alignment (GMA) , 2007, J. Chem. Inf. Model..
[6] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.
[7] Ajay N. Jain,et al. Automatic identification and representation of protein binding sites for molecular docking , 1997, Protein science : a publication of the Protein Society.
[8] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[9] 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..
[10] W. Kabsch. A discussion of the solution for the best rotation to relate two sets of vectors , 1978 .
[11] Peter Willett,et al. RASCAL: Calculation of Graph Similarity using Maximum Common Edge Subgraphs , 2002, Comput. J..
[12] 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..
[13] Ian D. Walker,et al. Overview of damped least-squares methods for inverse kinematics of robot manipulators , 1995, J. Intell. Robotic Syst..
[14] R. A. Leibler,et al. On Information and Sufficiency , 1951 .
[15] Ajay N. Jain. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. , 2003, Journal of medicinal chemistry.
[16] Vicky Choi,et al. On Updating Torsion Angles of Molecular Conformations , 2006, J. Chem. Inf. Model..
[17] 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..
[18] Richard D. Taylor,et al. Improved protein–ligand docking using GOLD , 2003, Proteins.
[19] C. D. Gelatt,et al. Optimization by Simulated Annealing , 1983, Science.
[20] David S. Goodsell,et al. A semiempirical free energy force field with charge‐based desolvation , 2007, J. Comput. Chem..
[21] Didier Rognan,et al. Comparative evaluation of eight docking tools for docking and virtual screening accuracy , 2004, Proteins.
[22] W. Kabsch. A solution for the best rotation to relate two sets of vectors , 1976 .
[23] 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.
[24] C. Bystroff. An alternative derivation of the equations of motion in torsion space for a branched linear chain. , 2001, Protein engineering.
[25] Christopher W. Murray,et al. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model , 1998, J. Comput. Aided Mol. Des..
[26] Ajay N. Jain,et al. Parameter estimation for scoring protein-ligand interactions using negative training data. , 2006, Journal of medicinal chemistry.
[27] C. Venkatachalam,et al. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. , 2003, Journal of molecular graphics & modelling.
[28] R. Glen,et al. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. , 1995, Journal of molecular biology.
[29] N. Paul,et al. Recovering the true targets of specific ligands by virtual screening of the protein data bank , 2004, Proteins.
[30] Y.Z. Chen,et al. Ligand–protein inverse docking and its potential use in the computer search of protein targets of a small molecule , 2001, Proteins.
[31] Didier Rognan,et al. sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank , 2006, J. Chem. Inf. Model..
[32] Andreas Plückthun,et al. Docking small ligands in flexible binding sites , 1998 .
[33] Thomas Lengauer,et al. A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.
[34] 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..