| 1 |
Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010;31:671-690.
|
| 2 |
Velec HF, Gohlke H, Klebe G. 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. J Med Chem. 2005;48:6296-6303.
DOI
ScienceOn
|
| 3 |
Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD. Improved protein-ligand docking using GOLD. Proteins. 200 3;52:609-623.
DOI
ScienceOn
|
| 4 |
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem. 2004;25:1157-1174.
DOI
ScienceOn
|
| 5 |
Ekins S, Mestres J, Testa B. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br J Pharmacol. 2007;152:9-20.
DOI
ScienceOn
|
| 6 |
Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des. 1997;11:425-445.
DOI
ScienceOn
|
| 7 |
Gao Z, Li H, Zhang H, Liu X, Kang L, Luo X, Zhu W, Chen K, Wang X, Jiang H. PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics. 2008;9:104-110.
DOI
ScienceOn
|
| 8 |
Jenkins JL, Bender A, Davies JW. In silico target fishing: predicting biological targets from chemical structure. Drug Discov Today: Technologies. 2006;3:413-421.
DOI
ScienceOn
|
| 9 |
Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov. 2004;3:935-949.
DOI
ScienceOn
|
| 10 |
Lee M, Kim D. Large-scale reverse docking profiles and their applications. BMC Bioinformatics. 2012;13:S6.
|
| 11 |
Li H, Gao Z, Kang L, Zhang H, Yang K, Yu K, Luo X, Zhu W, Chen K, Shen J, Wang X, Jiang H. TarFisDock: a web server for identifying drug targets with docking approach. Nucl Acids Res. 2006;34:W219-224.
DOI
ScienceOn
|
| 12 |
Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil CR. Towards the development of universal, fast and highly accurate docking/scoring methods: a long ways to go. Brit J Pharmacol. 2008;153:S7-S26.
|
| 13 |
Muegge I, Martin YC. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem. 1999;42:791-804.
DOI
ScienceOn
|
| 14 |
Nonell-Canals A, Mestres J. In silico target profiling of one billion molecules. Mol Inf. 2011;30:405-409.
DOI
ScienceOn
|
| 15 |
Oshiro CM, Kuntz ID, Dixon JS. Flexible ligand docking using a genetic algorithm. J Comput Aided Mol Des. 1995;9:113-130.
DOI
|
| 16 |
Sinko W, Lindert S, McCammon JA. Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des. 2013;81:41-49.
DOI
ScienceOn
|
| 17 |
Paul N, Kellenberger E, Bret G, Muller P, Rognan D. Recovering the true targets of specific ligands by virtual screening of the protein data bank. Proteins. 2004;54:671-680.
DOI
ScienceOn
|
| 18 |
Rognan D. Structure-based approaches to target fishing and ligand profiling. Mol Inf. 2010;29:176-187.
DOI
ScienceOn
|
| 19 |
Shoichet BK, McGovern S, Wei B, Irwin JJ. Lead discovery using molecular docking. Curr Opin Chem Biol. 2002;6:439-446.
DOI
ScienceOn
|
| 20 |
Sussman JL, Lin D, Jiang J, Manning NO, Prilusky J, Ritter O, Abola EE. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr D Biol Crystallog r. 1998;1:1078-1084.
|
| 21 |
Taylor RD, Jewsbury PJ, Essex JW. A review of protein-small molecule docking methods. J Comput Aided Mol Des. 2002;16:151-166.
DOI
ScienceOn
|
| 22 |
Barlow DJ, Buriani A, Ehrman T, Bosisio E, Eberini I, Hylands PJ. In-silico studies in Chinese herbal medicines' research: evaluation of in-silico methodologies and phytochemical data sources, and a review of research to date. J Ethnopharmacol. 2012;140:526-534.
DOI
ScienceOn
|
| 23 |
Bohm HJ. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des. 1992;6:593-606.
DOI
|
| 24 |
Cai J, Han C, Hu T, Zhang J, Wu D, Wang F, Liu Y, Ding J, Chen K, Yue J, Shen X, Jiang H. Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and x-ray crystallography validation. Protein Sci. 2006;15:2071-2081.
DOI
ScienceOn
|
| 25 |
Canduri F, de Azevedo WF. Protein crystallography in drug discovery. Curr Drug Targets. 2008;9:1048-1053.
DOI
ScienceOn
|
| 26 |
Chrysina ED, Chajistamatiou A, Chegkazi M. From structure--based to knowledge--based drug design through x-ray protein crystallography: sketching glycogen phosphorylase binding sites. Curr Med Chem. 2011;18:2620-2629.
DOI
ScienceOn
|
| 27 |
Chen CYC. TCM database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico. PloS one. 2011;6:e15939.
DOI
ScienceOn
|
| 28 |
Chen YZ, Ung CY. Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach. J Mol Graph Model. 2001;20:199-218.
DOI
ScienceOn
|
| 29 |
Chen YZ, Zhi DG. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins. 2001;43:217-226.
DOI
|
| 30 |
Cramer RD 3rd, Patterson DE, Bunce JD. Recent advances in comparative molecular field analysis (CoMFA). Prog Clin Biol Res. 1989;291:161-165.
|
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