Analysis of comparative modeling predictions for CASP2 targets 1, 3, 9, and 17

Proteins: Structure, Function and Genetics

Volumn 29, Issue SUPPL. 1, 1997, Pages 68-73

  Harrison, Robert W ^a   Reed, Charles C ^a   Weber, Irene T ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

Distance restraints; Energy minimization; Homology modeling; Prediction errors; Protein structure

Indexed keywords

DIHYDROFOLATE REDUCTASE; GLUTATHIONE TRANSFERASE; PHOSPHOTRANSFERASE; PROTEIN; STELLACYANINE; UNCLASSIFIED DRUG; METALLOPROTEIN; SOLVENT; STELLACYANIN PROTEIN, PLANT; VEGETABLE PROTEIN;

ARTICLE; COMPUTER MODEL; CRYSTAL STRUCTURE; ERROR; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; PROTEIN CONFORMATION; RAT; SEQUENCE ALIGNMENT;

ANIMALS; GLUTATHIONE TRANSFERASE; METALLOPROTEINS; MODELS, MOLECULAR; PHOSPHOTRANSFERASES; PLANT PROTEINS; PROTEIN CONFORMATION; RATS; SEQUENCE ALIGNMENT; SOLVENTS; TETRAHYDROFOLATE DEHYDROGENASE;

EID: 0031301624     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0134(1997)1+<68::aid-prot10>3.0.co;2-p     Document Type: Article

References (14)

1. Mosimann, S., Meleshko, R., James, M.N.G. A critical assessment of comparative modeling of tertiary structures of proteins. Proteins 23:301-317, 1995.
2. Harrison, R.W., Chatterjee, D., Weber, I.T. Analysis of six protein structures predicted by comparative modeling techniques. Proteins 23:463-471, 1995.
3. Greer, J. Comparative modeling methods: Application to the family of mammalian serine proteases. Proteins 7:317-334, 1990.
4. Weber, I.T. Evaluation of homology modeling of HIV protease. Proteins 7:172-184, 1990.
5. Weber, I.T., Harrison, R.W. Molecular mechanics calculations on HFV-1 protease with peptide substrates correlate with experimental data. Protein Eng. 9:679-690, 1996.
6. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., et al. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
7. Flores, T.P., Orengo, C.A., Moss, D.S., Thornton, J.M. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci. 2:1811-1826, 1993.
8. Zegers, I., Maes, D., Dao-Thi, M.-H., Poortmans, F., Palmer, R., Wyns, L. The structures of RNase A complexed with 3′CMP and d(CpA): Active site conformation and conserved water molecules. Protein Sci. 3:2322-2339, 1994.
9. Weber, I.T., Harrison, R.W., Iozzo, R.V. Model structure of Decorin and implications for collagen fibrillogenesis. J. Biol. Chem. 271:31767-31770, 1996.
10. Harrison, R.W. Stiffness and energy conservation in the molecular dynamics: An improved integrator. J. Comp. Chem. 14:1112-1122, 1993.
11. Beulter, T.C., van Gunsteren, W.F. Molecular dynamics free energy calculation in four dimensions. J. Chem. Phys. 101:1417-1422, 1994.
12. Wlodawer, A., Nachman, J., Gilliland, G.L., Gallagher, W., Woodward, C. Structure of form III crystals of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 198:469-480, 1987.
13. Dixon, J.S. Evaluation of the CASP2 docking section. Proteins Suppl. 1:198-204, 1997.
14. Martin, A.C.R., MacArthur, M.W., Thornton, J.M. Assessment of comparative modeling in CASP2. Proteins Suppl. 1:14-28, 1997.