Chemistry Reference
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[316] Ritchie DW, Kemp GJL. Protein docking using spherical polar Fourier correlations. Proteins; Struct. Funct. Bionf. Genet
2000; 39:178-194.
[317] Putta S, Beroz P. Shapes of things:computer modeling of molecular shape in drug discovery. Curr. Top. Med. Chem.
2007; 27:1514-1524.
[318] Sutherland JJ, Nandigam RK, Erickson JA, Vieth M. Lessons in molecular recognition.2. Assessing and improving cross-
docking accuracy. J. Chem. Inf. Model. 2007;47:2293-2302.
[319] Mortier WJ, Van Genechten K, Gasteiger J. Electronegativity equalization-application and parametrization. J. Am. Chem.
Soc. 1985;107:829-835.
[320] Grishina MA, Bartashevich EV, Potemkin VA, Belik AV. Genetic algorithm for predicting structures and properties of
molecular aggregates in organic substances. J. Struct. Chem. 2002; 43:1040-1043.
[321] Bartashevic EV, Potemkin VA, Grishina MA, Belik AV. A method for multiconformation modeling of the three-
dimentsional shape of a molecule. J. Struct. Chem. 2002;43:1033-1039.
[322] Perola E. Minimizing false positives in kinase virtual screens. J. Chem. Theory Comput. 2006;64:422-435.
[323] Machicado C, Lopez-Llano J, Cuesta-Lopez, Bueno M and Sancho J. Design of ligand binding to an engineered protein
cavity using virtual screening and thermal up-shift evaluation. J. Comp.-Aided Mol. Des. 2005;19:421-443.
[324] Brenk R, Vetter SW, Boyce SE, Goodin DB and Shoichet BK. Probing molecular docking to a charged model binding
sitge. J.Mol. Biol. 2006;357:1449-1470.
[325] Musah RA, Jensen GM, Burke SW, Rosenfeld RJ and Goodin DB. Artificial protein cavities as specific ligand-binding
templates:characterization of an engineered heterocyclic catin-binding site that preserves the evolved specificity of the
parent protein. J. Mol. Biol. 2002; 315:845-857.
[326] Gohlke H and Klebe G. Statistical potentials and scoring functions applied to protein-ligand binding. Curr. Opin. Struct.
Biol. 2001;11:231-235.
[327] Nabuurs SB, Wagener M, de Vlieg J A flexible approach to induced fit docking. J. Med. Chem. 2007.49:5885-5594.
[328] Jorgensen WL. Efficient drug led discovery and optimization. Acc. Chem. Research. 2009; 42:724-733.
[329] Wei BQ, Weaver LH, Ferrari AM, Matthews BW and Schoichet BK. Testing a flexible-receptor docking algorithm in a
model binding site.J. Mol. Biol. 2004; 337:1161-1182.
[330] Chang CE and Gilson MK. Free energy entropy and induced fit in host-guest recognition :calculations with the second-
generation mining minima algorithm. J. Am. Chem. Soc. 2004; 126:13156-13164.
[331] Chen J, Lai L. Pocket v.2: Further developments on receptor-based pharmacophore modeling. J. Chem. Inf. Model.
2006;47:2684-2691.
[332] Jorgensen WL. The many roles of computation in drug discovery. Science 2004;303:1813-1818.
[333] Hagiwara Y and Tateno M. A novel computational scheme for acurate and efficient evaluation of π stacking. J. Phys
Condens. Matt. 2009;21:245103-245108.
[334] Congreve M, Chessari G, Tisi D, Woodhead AJ. Recent developments in fragment-based drug discovery. J. Med. Chem.
2008; 51:3361-3680.
[335] Das Debananda, Koh Yasuhiro, Tojo Y, Ghosh AK and Musuya H. Prediction of potency of protease inhibitors using free
energy simulations with polarizable quantum mechanics-based ligand and a hybrid water model. J. Chem. Inf. Mode
2009;49:2851-2862.
[336] Rao CB, Subramanian J and Sharma SD. Managing protein flexibility in docking and its applications. Drug Discovery
Today 2009;14:394-400.
[337] Subramanian J, Sharma S and B-Rao C. A novel computational analysis of ligand-induced conformational changes in the
ATP binding sites of cyclin dependent kinases. J. Med. Chem. 2006;49:5434-5441.
[338] Subramanian J, Sharma S, Chandrika BR. Modeling and selection of flexible proteins for structure-based drug
design:backbone and side chain movements in p38 MAPK. ChemMed Chem. 2008;3:336-344.
[339] Sherman W, Day T, Jacobson MP, Friesner RA and Farid R. Novel procedure for modeling ligand/receptor induced fit
effects. J. Med. Chem. 2006; 49:534-553.
[340] Cavasotto CN and Abagyan R. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol. Bio.
2004;337:209-225.
[341] Muegge I, Oloff S. Advances in virtual screening. Drug Discovery Today. Technol 2006; 3:405-411.
[342] Sousa SF, Fernandes PA, Ramos MJ. Protein-ligand docking:current status and future challenges. Proteins 2006;7:259-269.
[343] Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL III. Assessing scoring functions for protein-ligand interactions.J. Med.
Chem. 2004;47:3032-3407.
[344] Jacobson MP, Kaminski GA, Friesner RA and Rapp CS. Force field validation using protein side chain rediction . J. Phys.
Chem. B 2002;106:11673-11680.
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