Efficient dynamics in the space of contact maps

Folding and Design

Volumn 3, Issue 5, 1998, Pages 329-336

  Vendruscolo, Michele ^a   Domany, Eytan ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Contact map; Dynamics; Energy minimization; Protein folding

Indexed keywords

PROTEIN;

ARTICLE; DYNAMICS; ENERGY; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

EID: 0031728015     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(98)00045-5     Document Type: Article

References (26)

1. Mirny, L. & Domany, E. (1996). Protein fold recognition and dynamics in the space of contact maps. Proteins 26, 391-410.
2. Vendruscolo, M., Kussell, E. & Domany, E. (1997). Recovery of protein structure from contact maps. Fold. Des. 2, 295-306.
3. Domany, E., Najmanovich, R. & Vendruscolo, M. (1998). Protein folding in the space of contact maps. In Proceedings of the HLRZ Workshop on Monte Carlo Approach to Biopolymers and Protein Folding (Barkema, G., Grassberger, P. and Nadlers, W., eds) World Scientific.
4. Chan, H.S. & Dill, K.A. (1990). Origins of structure in globular proteins. Proc. Natl Acad. Sci, USA 87, 6388-6392.
5. Godzik, A., Skolnik, J. & Kolinski, A. (1993). Regularities in interaction patterns of globular proteins. Protein Eng. 6, 801-810.
6. Holm, L & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 23-138.
7. Hinds, D.A. & Levitt, M. (1994). Exploring conformational space with a simple lattice model for protein structure. J. Mot. Biol. 243, 668-682.
8. Crippen, G. & Havel, T.F. (1988). Distance Geometry and Molecular Conformation. Wiley, New York.
9. Brünger, AT., Clore, G.M., Gronenborn, A.M. & Karplus, M. (1986). Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl Acad. Sci. USA 83, 3801-3805.
10. Chan, H.S. & Dill, K.A. (1991). "Sequences space soup" of proteins and copolymers. J. Chem. Phys. 35, 3775-3787.
11. Šali, A., Shakhnovich, E.I. & Karplus, M. (1994). Kinetics of protein folding. J. Mol. Biol. 235, 1614-1636.
12. Kandel, D. & Domany, E. (1991). General cluster Monte Carlo dynamics. Phys. Rev. B 43, 8539-8555.
13. Evertz, H.G., Hasenbush, M., Marcu, M., Pinn, K. & Solomon, S. (1991). High precision measurement of the SOS surface thickness in the rough phase. J. Phys. I (France) 1, 1669-1674.
14. Chothia, C. (1992). One thousand families for the molecular biologist. Nature 357, 543-544.
15. Orengo, C.A., Jones, D.T. & Thornton, J.M. (1994). Protein superfamilies and domain superfolds. Nature 372, 631-634.
16. Orengo, C.A., et al., & Thornton, J.M. (1997). CATH - a hierarchical classification of protein domain structures. Structure 5, 1093-1108.
17. Rost, B. & Sander, C. (1993). Improved prediction of protein secondary structure by use of sequence profile and neural networks. Proc. Natl Acad. Sci. USA 90, 7558-7562.
18. Garnier, J., Gibrat, J.F. & Robson, B. (1996). GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. 266, 540-553.
19. Stauffer, D. & Aharony, A. (1992). Introduction to Percolation Theory. Second Edition, Taylor & Francis, London.
20. Chakrabartty, A. & Baldwin, R.L. (1995). α-Helix stability. Adv. Protein Chem. 46, 141-176.
21. de Gennes, P.G. (1979). Scaling Concepts in Polymer Physics. Cornell University Press, Ithaca, NY.
22. Munoz, V., Thompson, P.A., Hofrichter, J. & Eaton, W.A. (1997). Folding dynamics and mechanism of β-hairpin formation. Nature 390, 196-199.
23. Wolff, U. (1989). Comparison between cluster Monte Carlo algorithms in the Ising model. Phys. Lett. B228, 379-382.
24. Taketomi, H., Ueda, Y. & Gō, N. (1975). Studies of protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int. J. Peptide Protein Res. 7, 445-459.
25. Elofsson, A., Le Grand, S.M. & Eisenberg, D. (1995). Local moves: an efficient algorithm for simulation of protein folding. Proteins 23, 73-82.
26. 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.