Protein folding simulation with genetic algorithm and supersecondary structure constraints

Proteins: Structure, Function and Genetics

Volumn 31, Issue 3, 1998, Pages 247-257

  Cui, Yan ^a   Chen, Run Sheng ^a   Wong, Wing Hung ^b  

^a INSTITUTE OF BIOPHYSICS   (China)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Genetic algorithm; Hydrophobic potential; Protein structure prediction; Solvent accessible surface area; Supersecondary structure

Indexed keywords

ALGORITHM; ARTICLE; CALCULATION; CRYSTAL STRUCTURE; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SIMULATION; STRUCTURE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOLVENTS;

EID: 0009636533     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980515)31:3<247::AID-PROT2>3.0.CO;2-G     Document Type: Article

References (54)

1. Richards, F.M. Areas, volumes, packing, and protein structures. Annu. Rev. Biophys. Bioeng. 6:151-176, 1977.
2. Kauzmann, W. Some factors in the interpretation of protein denaturation. Adv. Prot. Chem. 14:1-64, 1959.
3. Dill, K.A. Dominant forces in protein folding. Biochemistry 29:7133-7155, 1990.
4. Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Thomas, P.D., Chan, H.S. Principle of protein folding - A perspective from simple exact models. Protein Sci. 4:561-602, 1995.
5. Eisenberg, D., Weiss, R.M., Terwillinger, T.C. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. USA 81:140-144, 1984.
6. Crippen, G.M. The tree structural organization of proteins. J. Mol. Biol. 126:315-332, 1978.
7. Rose, G.D. Hierarchic organization of domains in globular proteins. J. Mol. Biol. 134:447-470, 1979.
8. Wetlaufer, D. Nucleation, rapid folding, and globular interchain regions in proteins. Proc. Natl. Acad. Sci. USA 70:697-701, 1973.
9. Levinthal, C. Are there pathways in protein folding? J. Chem. Phys. 65:44-45, 1968.
10. Unger, R., Moult, J. Finding the lowest free energy conformation of a protein is a NP-hard problem: Proof and implication. Bull. Math. Biol. 55:1183-1198, 1993.
11. Sun, Z., Rao, X., Peng, L., Xu, D. Prediction of protein supersecondary structures based on the artificial neural network method. Protein Eng. 10:763-769, 1997.
12. Sun, S., Thomas, P.D., Dill, K.A. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng. 8:769-778, 1995.
13. Srinivasan, R., Rose, G. LINUS: A hierarchic procedure to predict the fold of a protein. Proteins 22:81-99, 1995.
14. Yue, K., Dill, K.A. Folding proteins with a simple energy function and extensive conformational searching. Protein. Sci. 5:254-261, 1996.
15. Topham, C.M., McLeod, A., Eisenmenger, F., Overington, J.P., Johnson, M.S., Blundell, T.L. Fragment ranking in modelling of protein structure: Conformationally constrained environmental amino acid substitution tables. J. Mol. Biol. 229:194-220, 1993.
16. Sun, Z., Jiang, B.J. Patterns and conformations commonly occurring supersecondary structures (basic motifs) in Protein Data Bank. J. Protein Chem. 15:675-690, 1996.
17. Lee, B., Richards, F.M. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55:379-400, 1971.
18. Shrake, A., Rupley, J.A. Environment and exposure to solvent of protein atoms: Lysozyme and insulin. J. Mol. Biol. 79:351-371, 1973.
19. Richarmond, T.J., Richards, F.M. Packing of α-helices: Geometrical constraints and contact areas. J. Mol. Biol. 119:537-555, 1978.
20. Finney, J.L. Volume occupation, environment, and accessiblity in proteins: Environment and molecular area of RNase-S. J. Mol. Biol. 119:415-441, 1978.
21. Greer, J., Bush, B. Macromolecular shape and surface maps by solvent exclusion. Proc. Natl. Acad. Sci. USA 75:303-307, 1978.
22. Pearl, L.H., Honegger, A. Generation of molecular surfaces for graphic display. J. Mol. Graph. 1:9-12, 1983.
23. Mueller, J.J. Calculation of scattering curves for macromolecules in solution and comparison with results of methods using effective atomic scattering factors. J. Appl. Cryst. 16:74-82, 1983.
24. Pavlov, M. Y., Fedorov, B.A. Improved technique for calculating X-ray scattering intensities in solution: Evaluation of the form, volume, and surface of a particle. Biopolymers 22:1507-1522, 1983.
25. Lorensen, W., Cline, H. Marching cubes: A high resolution 3D surface construction algorithm. Comput. Graph. 21:163-169, 1987.
26. Meyer, A.Y. Molecular mechanics and molecular shape. V. On the computation of the bare surface area of molecules. J. Comp. Chem. 9:18-24, 1988.
27. Karfunkel, H.R., Eyrand, V. An algorithm for the representation and computation of supermolecular surfaces and volumes. J. Comp. Chem. 10:628-634, 1989.
28. Connolly, M.L. Analytical molecular surface calculation. J. Appl. Cryst. 16:548-558, 1983.
29. Richmond, T.J. Solvent accessible surface area and excluded volume in proteins: Analytical equations for overlapping spheres and implications for the hydrophobic effect. J. Mol. Biol. 178:63-89, 1984.
30. Connolly, M.L. Molecular surface triangulation. J. Appl. Cryst. 18:499-505, 1985.
31. Gibson, K.D., Scheraga, H.A. Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii. Mol. Phys. 62:1247-1265, 1987.
32. Gibson, K.D., Scheraga, H.A. Surface area of the intersection of three sphere with unequal radii: a simplified analytical formula. Mol. Phys. 64:641-644, 1988.
33. Dodd, L.R., Theodorou, D.N. Analytical treatment of the volume and surface area of molecules formed by an arbitrary collection of unequal spheres intersected by planes. Mol. Phys. 72:1313-1345, 1991.
34. Wang, H., Levinthal, C. A vectorized algorithm for calculating the accessible surface area of macromolecules. J. Comp. Chem. 12:868-871, 1991.
35. Pascual-Ahuir, J.L., Silla, E. GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set. J. Comp. Chem. 11:1047-1060, 1991.
36. Silla, E.J., Tunon, I., Pascual-Ahuir, J.L. GEPOL: An improved description of molecular surfaces. II. Computing the molecular area and volume. J. Comp. Chem. 12:1077-1088, 1991.
37. Perrot, G., Cheng, B., Gibson, K.D., et al. MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives. J. Comp. Chem. 13:1-11, 1992.
38. LeGrand, S.M., Merz, K.M.M. Jr., Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables. J. Comp. Chem. 14:349-352, 1993.
39. Eisenhaber, F., Argos, P., Sander, C., Scharf, C. The double cubic lattice method: Efficent approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comp. Chem. 16: 273-284, 1995.
40. Totrov, M. The contour-buildup algorithm to calculate the analytical molecular surface. J. Struct. Biol. 116:138-143, 1996.
41. Ponder, J.W., Richards, F.M. Tertiary templates for proteins use of packing criteria in the enumeration of allowed sequences for different structural classes, J. Mol. Biol. 193:775-791, 1987.
42. Holland, J. "Adaptation in Natural and Artificial Systems." Ann Arbor, MI: University of Michigan Press, 1975.
43. Goldberg, D.E. "Genetic Algorithm in Search, Optimization and Machine Learning." Reading, MA: Addison-Wesley, 1989.
44. Unger, R., Moult, J. Genetic algorithm for protein folding simulation. J. Mol. Biol. 231:75-81, 1993.
45. Sun, S. Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms. Protein Sci. 2:762-785, 1993.
46. Bowie, J.U., Eisenberg, D. An evolutionary approach to folding proteins from sequence information: Application to small α-helical proteins. Proc. Natl. Acad. Sci. USA 91:4436-4440, 1994.
47. Dandekar, T., Argos, P. Folding the main chain of small proteins with the genetic algorithm. J. Mol. Biol. 236:844-861, 1994.
48. Pedersen, J.T., Moult, J. Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms. Proteins 23:454-460, 1995.
49. Pedersen, J.T., Moult, J. Protein folding simulations with genetic algorithms and a detailed molecular description. J. Mol. Biol. 269:240-259, 1997.
50. Wang, Y., Zhang, H., Li, W., Scott, R.A. Discriminating compact nonnative structures from the native structure of globular proteins. Proc. Natl. Acad. Sci. USA 92:709-713, 1995.
51. Huang, E.S., Subbish, S., Tsai, J., Levitt, M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J. Mol. Biol. 257:716-725, 1996.
52. Park, B., Levitt, M. Energy function that discriminate X-ray and near native folds from well-constructed decoys. J. Mol. Biol. 258:367-392, 1996.
53. Chothia, C. Hydrophobic bonding and accessible surface area in proteins. Nature 248:338-339, 1974.
54. Eisenberg, D., McLanchlan, A.D. Solvation energy in protein folding and binding. Nature 319:199-203, 1986.