Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches

Journal of Molecular Biology

Volumn 235, Issue 5, 1994, Pages 1598-1613

  Kocher, Jean Pierre A ^a   Rooman, Marianne J ^a   Wodak, Shoshana J ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Potential functions; Protein data bases; Protein structure prediction

Indexed keywords

EID: 0028318094     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1994.1109     Document Type: Article

References (39)

1. Bernstein, F., Koetzle, T., Williams, G., Meyer, K., Iiriee, M., Rodgers, J., Kennard, O., Shhnanoushi, T. & Tasumi, M. (1977). The protein data bank: a computer-based archival file for maoroniolecular structures. J. Mol. Biol. 112. 535-542.
2. Bowie, J. U., Liithv, R. & Risen berg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science., 253, 164-170
3. Bryant, S. H. & Lawrence, O. 17. (1993). An empirical energy function for threading protein sequence through folding motif. Proteins, 16. 92-112
4. Casari, G. & Sippi, M. I. (1992). Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. J. Mol. Biol. 224, 725-732.
5. Ghothia, C. (1992). One thousand protein families for the molecular biologist. Nature (fumdan). 357. 543-544.
6. Chothia, C. & Janin, J. (1975). Principles of protein-protein recognition. Nature (London), 256, 705-708.
7. Covell, D. G. (1992). Folding protein a-carbon chains into compact forms by Monte Carlo methods. Proteins, 14, 409-520.
8. Fetrow, J. S. & Bryant, S. H. (1993). New programs for protein tertiary structure prediction. Bio J Technology, 11.479-484.
9. Friedrichs, M. S., Goldstein, R. A. & Wolynes, P. G. (1991). Generalized protein tertiary structure recognition using associative memory hamiltonians. J. Mol. Biol. 222, 1013-1034.
10. Gibrat, J.-F., Robson, B. & Gamier, J. (1987). Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J. Mol. Biol. 198, 425-443.
11. Godzik, A. & Skolnick, J. (1992). Sequence-structure matching in globular proteins: application to super-secondary and tertiary structure determination. Proc. Nat. Amd. Sci., U.S.A. 89, 98-102.
12. Godzik, A., Kolinski, A. & Skolnick, J. (1992). A topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol. 227, 227-238.
13. Goldstein, R. A., Luthev-Schulten, Z. A. & Wolynes, P. G. (1992a). Protein tertiary structure recognition using optimized hamiltonians with local interactions. Pror. Nat. Acad. Sci., U.S.A. 89. 9029-9033.
14. Goldstein, R. A., Luthey-Kehulten, Z.A, & Wolynes, P. G. (1992b) Optimal protein-folding codes from spin-glass theory. Pror. Nat. Acad. Sci., U.S.A. 89, 4918-4922.
15. Hendlich, M., Lackner, P., Weitekus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G. & Sippl, M. (1990). Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 216. 167-180.
16. Huysmans, M., Richelle, J. & Wodak, S. J. (1991). SESAM, a relational database for structure and sequence of macromolecules. Proteins, 11, 59-76.
17. Janin, J., Wodak, S. J., Levitt, M. & Maigret, B. (1978). Conformation of amino acid side-chains in proteins. J. Mol. Biol. 125, 357-386.
18. Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). A new approach to protein fold recognition. Nature (London), 358, 86-89.
19. Kang, H. S., Kurochkina, N. A. & Lee, B. (1993). Estimation and use of protein backbone angle probabilities. J. Mol. Biol. 229, 448-460.
20. Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55. 379-400.
21. Levitt, M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104, 59-107.
22. Maiorov, V. N. & Crippen, G. M. (1992). A contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 221, 876-888.
23. Miller, S., Janin, J., Lesk, A. M. & Chothia, C. (1987). Interior, surface of monomeric proteins. J. Mol. Biol. 196, 641-656.
24. Miyazawa, B. & Jernigan, R. L. (1985). Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18, 534-552.
25. M orris, A. L., MacArthur, M. W., Gail Hutchinson, E. & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins, 12, 345-364.
26. Novotny, J., Bruccoleri, R. & Karplus, M. (1984). An analysis of incorrectly folded protein models. Implications for structure predictions. J. Mol. Biol. Vol III, 787-818.
27. Ouzo unis, C., Sander, C., Scharf, M. & Schneider, R. (1993). Prediction of protein structure by evaluation of sequence-structure fitness: aligning sequences to contact profiles derived from 3D structures. J. Mol. Biol. 232, 805-825.
28. Ponder, J. W. & Richards, F. M. (1987). Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193, 775-791.
29. Ramachandran, G. & Sasisekharan, V. (1968). Conformation of polypeptides and proteins. Advan. Protein Chem. 23, 283-437.
30. Rooman, M. D. & Wodak, S. J. (1988). Identification of predictive sequence motifs limited by protein structure data base size. Nature (London), 335, 45-49.
31. Rooman, M. J., Kocher, J.-P. A. & Wodak, S. J. (1991). Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. J. Mol. Biol. 211. 961-979.
32. Rooman, M. J., Kocher, J.-P. A. & Wodak, S. J. (1992). Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry, 31, 10226-10238.
33. Sippl, M. (1990). Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859-883.
34. Sippl, M. J. (1993). Boltzmann’s principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structure. J. Comp. Aided Mol. Design, 7, 473-501.
35. Sippl, M. J. & Weitekus, S. (1992), Detection of nativelike models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins, 13, 258-271.
36. Wilmanns, M. & Eisenberg, D. (1993). 3D profiles from residue-pair preferences: identification of sequences with JiJa-barrel fold. Proc. Nat. Acad. Sci., U.S.A. 90, 1379 1383.
37. Wilson, C. & Doniach, S. (1989). A computer model to dynamically simulate protein folding: studies with crambin. Proteins, 6, 193-209.
38. Wodak, S. J. & Janin, J. (1980), Analytical approxima-t-ion to the accessible surface area of proteins. Proc. Nat. Acad. Sci., U.S.A. 77, 1736-1740.
39. Wodak, S. J. & Rooman, M. J. (1993). Generating and testing protein folds. Curr. Opin. Struct. Biol. 3, 247-259.