Chemistry Reference
In-Depth Information
[351] Liu Yl and Wang R. Test MM-PB/SA on true conformational ensembles of protein-ligand
complexes, J. Chem. In. Model. 2010, 50: 1682-1692.
[352] Xiang M, Cao Y, Fan W, Chen L and Mo Y Compuer-aided drug design:Lead discovery
and optimizations, Combinatorial chemistry & high throughput screening, 2012, 15:328-
337.
[353] Gohike H, Klebe G. Approaches to the description and prediction of the leading binding
affinity of small-molecule ligands to macromolecular receptors. Angew. Chem. Int. Ed.
2002, 41, 15:2644-2676.
[354] Song CH, Lim SJ and Tang JC, Recent advances in computer-aided drug design, Briefings
in bioinformatics, 2009, 10:579-591.
[355] Huang SY, Grinter SZ and Zou X, Scoring functions and their evaluation methods for
protein-ligand docking: recent advances and future directions, Phys. Chem Chem. Phys
2010,12:12899-12098.
[356] Kawatkar S, Mustakas D, Miller M and McCarthy DJ, Virtual fragment screening:
exploration of MM-PBSA rescoring, J. Comput. Aided Mol. Des. 2013, 26:921-914.
[357] Wang W, He W, Zhou X and Chen X, Optimization of molecular docking score with
support vector rank regression, Proteins, 2013, 81: 1386-1398.
[358] Hsieh JH, Yin S, Wang XS, Liu, Dokholyan NV and Tropsha A, Chemoinformatics meets
molecular mechanics: A combined application of knowledge-based pose scoring and
physical force field-based hit scoring functions improves the accuracy of structure-based
virtual screening. J. Chem. Inf. And Model. 2012, 52: 16-28.
[359] Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK and Sali A, Statistical
potential for modeling and ranking of protein-ligand interactions, J. Chem. Information and
Modeling, 2011, 51:3078-3092.
[360] Pauli dos Santos RN, Rostirolla DC, Martinelli LK, Ducati RG, Timmers LFSM, Basso
LA, Santos DS, Guido RVC, Andricopulo AD and de Souza ON, Discovery of new
inhibitors of mycobacterium tuberculosis enzyme using virtual screening and a 3d-
pharmacophore-based approach, J. Chem. Inf. and modeling, 2013,43: 2390-2401.
[361] Ma XH, Zhu F, Liu X, Shi Z, Zhang JX, Yang SY, Wei YQ and Chen YZ. Virtual
screening methods as tools for drug lead discovery from large chemical libraries, Current
medicinal chemistry, 2012, 19: 5562-5571.
[362] Christ CD, Mark AE, van Gunsteren WF. Basic ingredients of the free energy calculations:
a review. J. Comput. Chem. 2010, 31: 1469-1582.
[363] Deng Y, Roux B. Computations of standard binding free energies with molecular dynamics
simulations. J. Phys Chem. B, 2009, 113: 2245-2246.
[364] Phillips JC, Braun R, Wang W, Gumbart J, Tajkorshid E, Villa E, Chipot C, Skeel RD,
Kale L, Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 2005,
26:1781-1802.
[365] DiMaio F, Terwilliger TC, Read RJ, Wlodaver A, Oberdorfer G, Wagner U,Valikov E,
Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwai H, Pokkuluri PR, Baker D.
Improved molecular replacement by density-and energy-guided protein structure
optimization. Nature, 2011, 473: 540-543.
[366] Taft CA, Silva CHTP, State of the art in quantum mechanics based methods in drug design,
Chapter 1, New developments in Medicinal Chemistry, Bentham Science Publishers, 2010
Eds. (Bentham Science, U.A.E.) pp 1-56.
[367] Ball P. Water as an active constituent in cell biology. Chem. Rev 2008, 108:74-108.
