Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions

Protein Science

Volumn 7, Issue 12, 1998, Pages 2578-2586

  Keskin, O ^a   Bahar, I ^a,b   Badretdinov, A Y ^c,d   Ptitsyn, O B ^b,d   Jernigan, R L ^b  

^a BOGAZICI UNIVERSITY   (Turkey)

^b NATIONAL CANCER INSTITUTE   (United States)

^c ROCKEFELLER UNIVERSITY   (United States)

^d INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

Knowledge based potentials; Protein interfaces; Protein solvation

Indexed keywords

ARTICLE; COMPLEX FORMATION; ELECTRIC POTENTIAL; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; STATISTICAL ANALYSIS; SURFACE PROPERTY;

EID: 0031678069     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560071211     Document Type: Article

References (25)

1. Bahar I, Jernigan RL. 1996. Coordination geometry of non-bonded residues in globular proteins. Fold Des 1:357-370.
2. Bahar I, Jernigan RL. 1997. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 266:195-214.
3. Bahar I, Kaplan M, Jernigan RL. 1997. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 29:292-308.
4. Bernstein F, Koetzle T, Williams G, Meyer E, Brice M, Rodgers J, Kennard O, Shimanouchi T, Tasumi M. 1977. The protein databank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
5. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. 1995. Principles of protein folding. A perspective from simple exact models. Protein Sci 4:562-602.
6. Finkelstein AV, Badretdinou AY, Gutin AM. 1995. Why do protein architectures have a Boltzmann-like statistics? Proteins 23:142-150.
7. Huber T, Torda AE. 1998. Protein fold recognition without Boltzmann statistics or explicit physical basis. Protein Sci 7:142-149.
8. Jernigan RL, Bahar I. 1996. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 6:195-209.
9. Jones DT, Thornton JM. 1996. Potential energy functions for threading. Curr Opin Struct Biol 6:210-216.
10. Kocher J-PA, Rooman MJ, Wodak S. 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 235:1598-1613.
11. Li H, Tang C, Wingreen NS. 1997. Nature of driving force for protein folding: A result from analyzing the statistical potential. Phys Rev Lett 79:765-768.
12. Lijnzaad P, Argos P. 1997. Hydrophobic patches on protein subunit interfaces: Characteristics and prediction. Proteins 28:333-343.
13. Mirny L, Shakhnovich E. 1996. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 204:1164-1179.
14. Miyazawa S, Jernigan RL. 1985. Estimation of effective inter-residue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552.
15. Miyazawa S, Jernigan RL. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256:623-644.
16. Park B, Levitt M. 1996. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 258:367-392.
17. Sippl MJ. 1995. Knowledge-based potentials for proteins. Curr Opin Struct Biol 5:229-235.
18. Skolnick J, Jaroszewski L, Kolinski A, Godzik A. 1997. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 6:676-688.
19. Thomas PD, Dill KA. 1996. Statistical potentials extracted from protein structures: How accurate are they? J Mol Biol 257:457-469.
20. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
21. Torda AE. 1997. Perspectives in protein fold recognition. Curr Opin Struct Biol 7:200-205.
22. Tsai C, Nussinov R. 1997. Hydrophobic folding units at protein-protein interfaces: Implications to protein folding and protein-protein association. Protein Sci 6:1426-1437.
23. Tsai C, Xu D, Nussinov R. 1997. Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes. Protein Sci 6:1793-1805.
24. Young L, Jernigan RL, Covell DG. 1994. A role for surface hydrophobicity in protein-protein recognition. Protein Sci 3:717-729.
25. Zhang L, Skolnick J. 1998. How do potentials derived from structural databases relate to "true" potentials? Protein Sci 7:112-122.