Chemistry Reference
In-Depth Information
[206] Eilmes A and Kubisiak P. Relative complexation energies for Li
+
ion in solution:molecular level solvation versus
polarizable continuum model study. J. Phs. Chem A. 2010. DOI 10.1021/jp9077359a
[207] Kelly CP, Cramer CJ and Truhlar DG. Aqueous solvation free energies of ions and ion-water clusters based on an accurate
value for the absolute aqueous solvation free energy of the proton. 2006;110:16066-16081.
[208] Chen JM, Xu SL, Wawrzaj ZM Basaab GS, Jordan DB. Structure-based design of potent inhibitors of scytalone dehydrase
displacement of a water molecule from the active site. Biochemistry 1998;37:17735-1774.
[209] Holdgate GA, Tunnincliffe A, Ward WHJ, Weston SA, Rosenbrock G, Barth PT, Taylor IWF, Pauptit RA, Timms D. The
entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA
gyrase: a thermodynamic and crystallographic study. Biochemistry 1997;36:9963-9673.
[210] Teramoto R, Fukunishi H. Supervised consensus scoring for docking and virtual screening. J. Chem. Inf. Model.
2007:47:526-534.
[211] Mikol V, Papageorgious C, Borer X. The role of water molecules in the structure-based design of (5-hydroxnorvaline) 2-
cyclosporine-synthesis, biological activity and crystallographic analysis with cyclophilin-A. J. Med. Chem. 1995;36:3361-
3367.
[212] Picket SD, Sherborne BS, Wilkinson T, Bennett J, Borkasakoti N, Boradhurst M, Hurst D, Kilford I, McKinnell M, Jones
PS, Discovery of novel low molecular weight inhibitors of IMPDH via virtual needle screening. Bioorg. Med. Chem. Lett.
2003;13:1691-1694.
[213] Mancera RL. De novo ligand design with explicit water molecules:an application to bacterial enuraminadase. J. Comput-
Aided Mol.Des. 2002;16-479-499.
[214] Garcia-Sosa AT, Mancera RL. The effect of tightly-bound water molecules on scaffold diversity in the computer-aided de
novo ligand design of CKD-2 inhibitors. J. Mol. Model. 2006;12:422-431.
[215] Cherbavaz DB, Lee ME, Sroud RM, Koschi DE. Active site water molecules revealed in the 2.1 angstrom resolution
structure of a site-directed mutant of isocitrate dehydrogenase. J. Mol. Biol. 2000;295:377-385.
[216] Garcia-Sosa AT, Firth-Clark S, Mancera RL. Including tightly-bound water molecules in de novo drug design.
Exemplification through the in silico generation of poly(ADP-ribose)polylmerase ligands. J. Chem. Inf. Model.
2005;45:624-633.
[217] Rarey J, Kramer B, Lengauer T. The particle concept:placing discrete water molecules during proton-ligand docking
predictions. Proteins 1999;34;17-28.
[218] Taha MO, Dahabiyeh LA, Bustanji Y, Zalhoum H, Saleh S. Combining ligand-based pharmacophore modeling, QSAR
analysis and in-silico screening for the discovery of new potent hormone sensitive lipase inhibitors. J. Med. Chem. 2008;
51:6478-6494.
[219] Rao MS, Olson AJ. Modelling of inhibitor complexes:A computational flexible docking approach. Proteins 1999;34:173-183.
[220] Minke WE, Diller DJ, Hol WG, Verlinde CL. The role of waters in docking strategies with incremental flexibility for
carbohydrate derivatives:heat-labile enterotoxin, a multivalent test case. J. Med. Chem. 1999;42:1778-1788.
[221] Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS. Automated docking to multiple target
structures:incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002;46:34-40.
[222] Floriano WB, Vaidehi N, Zamanakos G, Goddard WA, III. Hier VLS. Hierarchical docking protocol for virtual ligand
screening of large-molecule databases. J. Med. Chem. 2004;47, 56-71.
[223] Bellocchi D, Macchianulo A, Constantino G, Pellicciar R. Docking studies on PARP-1 inhibitors:insights into the role of a
binding pocket water molecule. Bioorg. Med. Chem. 2005; 13:1151-1157.
[224] Yang JM, Chen CC. GEMDOCK: A generic evolutionary method for molecular docking. Proteins 2002;55:288-304.
[225] de Graaf C, Pospisil P, Wouter P, Folkers G, Venneule NPE. Binding mode prediction of cytochrome P450 and thymidine
kinase protein-ligand complexes by consideration of water and rescoring in automated docking. J. Med. Chem.
2005;48:2308-2318.
[226] Verdonk ML, Chessari G, Cole JC, Hartshorn MJ, Murray CW, Nisink JWM, Taylor RD, Taylor R. Modeling water
molecules in protein-ligand docking using GOLD. J. Med. Chem. 2005;48:6504-6515
[227] de Graff C, Oostenbrink C, Keizers PHJ, van der Wijst T, Jongejan A, Vermeulen NPE. Catalytic site prediction and
virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. J.
Med. Chem. 2006;49:2417-2430.
[228] Harsborn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortenson PN, Murray CW. Diverse, high-quality
test set for the validation of protein-lignd docking performance. J. Med. Chem. 2007;50:726-741.
[229] de Graff C, Oostenbrink NPE. Catalytic side prediction and virtual screening of cytochrome P450 2D6 substrates by
consideration of water and rescoring in automated docking. J Med. Chem. 2006,49:2417-2430.
[230] Mancer RL, Kallblad PK, Todorov NP. Ligand-protein docking using a quantum stochastic tunneling optimization
method. J. Comput. Chem. 2004;25:858-864.
