Chemistry Reference
In-Depth Information
[536] Fang J, Huang D, Zhao W, Ge H, Luo HB and Xu J, A new protocol for predicting Novel
GSK-3β ATP competitive inhibitors, Chem. Information and Modeling, 2011, 51: 1451-
1438.
[537] Luo W, Pei J, Zhu Y, A fast protein-ligand docking alrithm based on hydrogen bond
matching and surface shape complementarity, J. Mol. Model. 2010, 16: 903-913.
[538] Shin WH and Seok C, GalaxyDock:Protein-ligand docking with flexile protein sidechains,
Chem. Inf. And Modeling, 2012, 52: 3225- 3232.
[539] Alisaraie L, Haller LA and Fels G, A QXP-based multistep docking procedure for accurate
prediction of protein-ligand complexes, J. Chem. Info. Model, 2006, 46:1174-1187.
[540] Parenti MD, Rastelli G, Advances and applications of binding affinity prediction methods
in durg discovery, Biotechnology Advances, Biotechnology Advances, 2012, 30:244-250.
[541] Antes I, DynaDock: A new molecular dynamics-based algorithm for protein-peptide
docking including receptor flexibility, Proteins, 2010, 78:1084-1104.
[542] Okamato M, Masuda Y, Muroya A, Yasuno K, Takahashi O and Furuya T, Evaluation of
docking calculation on X-ray structures using Consensus-Dock, Chem. Pharm Bull, 2010,
58: 1655 - 1657.
[543] Molecular Operating Environment (MOE), 2013.08; Chemical Computing Group Inc.,
1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2013.
[544] Labute P, Williams C. Feher M, Sourial E, Schmidt JM. Flexible Alignment of Small
Molecules; J. Med. Chem. 2001, 44: 1483-1490.
[545] Abad-Zapatero C, Chapter 8- Sightseeing Chemicobiological Space, In Ligand Efficiency
Indices for Drug Discovery; Academic Press (2013) pp 109-149.546
[546] Molegro Virtual Docker 5.5
(http://www.clcbio.com).
[547] Muegge I and Martin YC. A general and fast scoring function for protein-ligand
interactions J. Med. Chem. 1999, 42:791-804.
[548] Huang SY and Zou X. Inclusion of solvation and entropy in the knowled-based scoring
functions for protein-ligand interactions. J. Chem. Inf. Model. 2010, 50: 262-273.
[549] Kroemer RT, Vulpetti A, McDonald JJ, Rohrer DC, Troset JY, Giordanetto F, Cotesta S,
McMartin C, Kihlen M and Stouten PF. Assessment of docking poses: interactions-based
accuracy classification (IBAC)
versus
crystal structure derivations. J. Chem. In. Comput.
Sci. 2004, 44: 871-881.
[550] Yusuf D, Davis AM, Kleywegt GJ and Schmitt. An Alternative Method for the Evaluation
of Docking Performance: RSR
vs
. RMSD. J. Chem. Inf. Model. 2008, 48: 1411-1422.
[551] Baber JC, Thompson J, Cross B and Humblet C. Modeling and active site refinement for G
protein
‐
coupled receptors J. Chem. Inf. Model. 2009, 49: 1889-1900.
[552] Jain AN. J. Modeling and active site refinement for G protein
‐
coupled receptors. Comput-
Aided Mol. Des. 2000, 14:199-213.
[553] Liu J, He X and Zhang JZH. Improving the scoring of protein-ligand binding affinity by
including the effects of structural water and electronic polarization. Chemical information
and modeling. 2013, 53, 1306−1314
[554] Wang W, He W, Zhou X and Chen X. Optimization of molecular docking scores with
support vector rank regression. Proteins. 2013, 81:1386-1398.
[555] Alder BJ, Wainwright TE, Phase transition for a hard-sphere systemJ Chem. Phys. 1957,
27:1208
[556] Gibson JB, Goland AN, Miligrim M and Vineyard GH, Dynamics of radiation damage.
Physics Rev.,1960, 120:1229.
