A survey of recent work on evolutionary approaches to the protein folding problem

Proceedings of the 1999 Congress on Evolutionary Computation, CEC 1999

Volumn 1, Issue , 1999, Pages 488-495

  Greenwood, Garrison W ^a   Shin, Jae Min ^b   Lee, Byungkook ^b   Fogel, Gary B ^c  

^a Western Michigan University   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c NATURAL SELECTION INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; EVOLUTIONARY ALGORITHMS; PROTEINS; SURVEYS;

COMPUTATIONAL BIOLOGY; EVOLUTION STRATEGIES; EVOLUTIONARY APPROACH; EVOLUTIONARY SEARCH ALGORITHMS; FUNCTIONAL CONFORMATIONS; MINIMAL FREE ENERGIES; NATIONAL CANCER INSTITUTE; PROTEIN FOLDING PROBLEM;

CONFORMATIONS;

EID: 77649285237     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.1999.781969     Document Type: Conference Paper

References (33)

1. D. E. Clark and D. R. Westhead. Evolutionary algorithms in computer-aided molecular design. J. Comput.-Aided Mol. Des., 10:337-358, 1996.
2. F. M. Richards. The protein folding problem. Sci. Amer., 264:54-63, 1991.
3. H. Chan and K. Dill. The protein folding problem. Physics Today, 46:24-32, 1993.
4. N. D. Socci, W. Bialek, and J. N. Onuchic. Properties and origins of protein secondary structure. Phys. Rev. E, 49:3440-3443, 1994.
5. E. E. Abola, J. L. Sussman, J. Prilusky, and N. O. Manning. Protein Data Bank Archives of Three-Dimensional Macromolecular Structures. In: Methods in Enzymology (C. W. Carter Jr. and R. M. Sweet, eds.), Vol. 277, Academic Press, San Diego, 1997.
6. A. Robertson and K. Murphy. Protein structure and the energetics of protein stability. Chem. Rev., 97:1251-1267, 1997.
7. G. W. Greenwood. Efficient construction of self-avoiding walks for protein folding simulations on a torus. J. Chem. Phys., 108:7534-7537, 1998.
8. M. J. Rooman, J-P. Kocher, and S. J. Wodak. Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochem., 31:10226-10238, 1992.
9. J. R. Gunn. Sampling protein conformations using segment libraries and a genetic algorithm. J. Chem. Phys., 106:4270-4281, 1997.
10. J. Pedersen and J. Moult. Protein folding simulations with genetic algorithms and a detailed molecular description. J. Mol. Biol., 269:240-259, 1997.
11. S. Sun, P. D. Thomas, and K. A. Dill. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Engr., 8:769-778, 1995.
12. C. Wilson, L. Gregoret, and D. Agard. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J. Mol. Biol., 229:996-1006, 1993.
13. N. Summers, W. Carlson, and M. Karplus. Analysis of side-chain orientations in homologous proteins. J. Mol. Biol., 196:175-198, 1987.
14. C. Notredame, L. Holm, and D Higgins. COFFEE: an objective function for multiple sequence alignments. Bioinfo., 14:407-422, 1998.
15. J. Desjarlais and T. Handel. De novo design of the hydrophobic cores of proteins. Protein Sci., 4:2006-2018, 1995.
16. G. Ghirlanda, J. Lear, A. Lombardi, and W. De-Grado. From synthetic coiled coils to functional proteins: automated design of a receptor for the calmodulin-binding domain of calcineurin. J. Mol. Biol., 281:379-391, 1998.
17. G. Morris, D. Goodsell, R. Huey, and A. Olson. Distributed automated docking of flexible ligands to proteins: parallel applications of Autodock 2.4. J. Comp.-Aid. Mol. Des., 10:293-304, 1996.
18. C. Rosin, R. Halliday, W. Hart, and R. Belew. A comparison of global and local search methods in drug docking. Proc. 7th ICGA, pages 221-228, 1997.
19. F. Solis and R. Wets. Minimization by random search techniques. Math. Ops. Res., 6:19-30, 1981.
20. G. Jones, P. Willett, R. Glen, A. Leach, and R. Taylor. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 267:727-748, 1997.
21. M. Raymer, P. Sanschagrin, W. Punch, S. Venkataraman, E. Goodman, and L. Kuhn. Predicting conserved water-mediated and polar ligand interactions in proteins using a k-nearestneighbors genetic algorithm. J. Mol. Biol., 265:445-464, 1997.
22. D. Gehlhaar, G. Verkhivker, P. Rejto, C. Sherman, D. B. Fogel, L. J. Fogel, and S. Freer. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem. Biol., 2:317-324, 1995.
23. F. Eisenmenger, P. Argos, and R. Abagyan. A method to configure protein side-chains from the main-chain trace in homology modeling. J. Mol. Biol., 231:849-860, 1993.
24. M. Vasquez. An evaluation of discrete and continuum search techniques for conformational analysis of side chains in proteins. Biopolymers, 36:53-70, 1995.
25. S. Schulze-Kremer and U. Tiedemann. Parameterizing genetic algorithms for protein folding simulation. Proc. 27th Ann. Hawaii Int'l Conf. on Sys. Sci., pages 345-354, 1994.
26. A. H. Kampen and L. M. Buydens. The ineffectiveness of recombination in a genetic algorithm for the structure elucidation of a heptapeptide in torsion angle space: a comparison to simulated annealing. Chem. & Intell. Lab. Sys., 36:141-152, 1997.
27. N. Krasnogor, D. Pelta, P. E. M. Lopez, and E. de la Canal. Genetic algorithm for the protein folding problem, a critical view. Proc. Engr. of Intell. Sys. 98, pages 345-352, 1998.
28. G. Ramachandran and V. Sasisekharan. Conformation of polypeptides and proteins. Adv. Protein Chem., 23:283-437, 1968.
29. P. J. Kraulis. Molscript-a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst., 24:946-950, 1991.
30. A. Elofsson, S. M. Le Grand, and D. Eisenberg. Local moves: an efficient algorithm for simulation of protein folding. Proteins, 23:73-82, 1995.
31. Y. Wang, H. Huq, X. de la Cruz, and B. Lee. A new procedure for constructing peptides into a given Cα chain. Folding & Design, 3:1-10, 1997.
32. S. Miyazawa and R. Jernigan. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18:534-552, 1985.
33. M. Sippl. 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, 1990.