Empirical entropie contributions in computational docking: Evaluation in APS reductase complexes

Journal of Computational Chemistry

Volumn 29, Issue 11, 2008, Pages 1753-1761

  Chang, Max W ^a   Belew, Richard K ^a,b   Carroll, Kate S ^c   Olson, Arthur J ^d   Goodsell, David S ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

^d SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

AutoDock; Computational docking; Configurational entropy; Empirical free energy force fields

Indexed keywords

APS REDUCTASE (APR); CLUSTER SIZES; COMPUTATIONAL DOCKING; LIGAND-PROTEIN COMPLEXES; LOCAL ENERGIES; MULTIPLE DOCKING; NUCLEOTIDE ANALOGUES; VIBRATIONAL ENTROPY;

BINDING ENERGY; DOCKING; EXPERIMENTS; FOOD ADDITIVES; NUCLEIC ACIDS; PHASE SHIFTERS; RISK ASSESSMENT;

CONFORMATIONS;

ADENYLYLSULFATE REDUCTASE; CARBOHYDRATE; LIGAND; OXIDOREDUCTASE;

ARTICLE; BINDING SITE; CHEMISTRY; CLUSTER ANALYSIS; EMPIRICAL RESEARCH; ENTROPY; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION;

BINDING SITES; CARBOHYDRATES; CLUSTER ANALYSIS; EMPIRICAL RESEARCH; ENTROPY; LIGANDS; OXIDOREDUCTASES ACTING ON SULFUR GROUP DONORS; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 47149102700     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20936     Document Type: Article

References (16)

1. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. J Comp Chem 1998, 19, 1639.
2. Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. J Comput Chem 2006, 28, 1145.
3. Sammon, J. W. IEEE Trans Comput 1969, C-18, 401.
4. Chang, C. E.; Chen, W.; Gilson, M. K. Proc Natl Acad Sci USA 2007, 104, 1534.
5. Rosenfeld, R. J.; Goodsell, D. S.; Musah, R. A.; Morris, G. M.; Goodin, D. B.; Olson, A. J. J Comp Aided Mol Des 2003, 17, 525.
6. Bottegoni, G.; Cavalli, A.; Recanatini, M. J Chem Inf Model 2006, 46, 852.
7. Ruvinsky, A. M.; Kozintsev, A. V. J Comput Chem 2005, 26, 1089.
8. Ruvinsky, A. M.; Kozintsev, A. V. Proteins Struct Funct Genet 2006, 62, 202.
9. Xiang, Z.; Soto, C. S.; Honig, B. Proc Natl Acad Sci USA 2002, 99, 7432.
10. Carroll, K. S.; Gao, H.; Chen, H.; Stout, C. D.; Leary, J. A.; Bertozzi, C. R. PLoS Biol 2005, 3, e250.
11. Chartron, J.; Carroll, K. S.; Shiau, C.; Gao, H.; Leary, J. A.; Bertozzi, C. R.; Stout, C. D. J Mol Biol 2006, 364, 152.
12. Hayes, J. M.; Stein, M.; Weiser, J. J Phys Chem A 2004, 108, 3575.
13. Head, M. S.; Given, J. A.; Gilson, M. K. J Phys Chem A 1997, 101, 1609.
14. Fersht, A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding; W. H. Freeman Company: New York, 1999.
15. Gasteiger, J.; Marsili, M. Tetrahedron 1980, 36, 3219.
16. Ruvinsky, A. M. J Comput Chem 2007, 28, 1364.