Design of reduced protein models by energy minimization using mathematical programming

Collection of Technical Papers - 10th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conference

Volumn 2, Issue , 2004, Pages 980-995

  Koh, Sung K ^a,b   Ananthasuresh, G K ^a,b   Croke, Christopher B ^a  

^a Department of Mechanical Engineering and Applied Mechanics ^*  (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTION-BASED INTERPOLATION; GAUSSIAN PROBABILITY DISTRIBUTION; LATTICE MODELS; QUADRATIC FORMULATION;

GRAPH THEORY; MATHEMATICAL PROGRAMMING; MONOMERS; OPTIMIZATION; PARAMETER ESTIMATION; PROTEINS;

AMINO ACIDS;

EID: 20344381321     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (30)

1. st ed, Oxford University Press, Oxford, New York, 2001, Chaps 1.
2. Deutsch, J. M. and Kurosky, T., "New algorithm for protein design," Phys. Rev. Letters, Vol. 76, 1996, pp. 323-326.
3. Sanjeev, B. S., Patra, S. M., and Vishveshwara, S., "Sequence design in lattice models by graph theoretical methods," J. Chem. Phys., Vol. 114, 2001, pp. 1906-1914.
4. Park, S., Yang, X. and Saven, J., "Advances in computational protein design," Curr. Opin. Struct. Biol. (2004 submitted)
5. Anfinsen, C., "Principles that govern the folding of protein chains," Science, Vol. 181, 1973, pp. 223
6. Zou, J. and Saven, J. G., "Statistical Theory of Combinatorial Libraries of Folding Proteins," J. Mol. Biol., Vol. 296, 2000, pp. 281-294.
7. Sun, S., Brem, R., Chan, H. S. and Dill, K. A., "Designing amino acid sequences to fold with good hydrophobic cores," Protein Eng., Vol. 8, 1995, pp. 1205-1213.
8. Jones, D. T., "De novo protein design using pairwise potentials and genetic algorithm," Protein Sci., Vol. 3, 1994, pp. 567-574.
9. Pande, V. S., Grosberg, A. Y. and Tanaka, T., "Protein superfamilies and domain super-folds," Nature, Vol. 372, 1994, pp. 631-634.
10. th Regional Meeting of the American Mathematical Society, Lawrenceville, NJ, April 17-19, 2004.
11. Koh, S. K. and Ananthasuresh, G. K., "A deterministic optimization approach to protein sequence design using continuous models," International Journal of Robotics Research, (2003 submitted)
12. Yue, K. and Dill, K. A., "Inverse protein folding problem: Designing polymer sequences", Proc. Natl. Acad. Sci. USA, Vol. 89, 1992, pp. 4163-4167.
13. Shaknovich, E. I. and Gutin, A. M., "Engineering of stable and fast-folding sequences of model proteins", Proc. Natl. Acad. Sci. USA, Vol. 90, 1993, pp. 7195-7199.
14. Yue, K., Fiebig, K. M., Thomas, P. D., Chan, H. S., Shaknovich, E. I. and Dill, K. A., "A test of lattice protein folding algorithms", Proc. Natl. Acad. Sci. USA, Vol. 92, 1995, pp. 325-329.
15. Miyazawa, S. and Jernigan, R., "Estimation of effective inter-residue contact energies from protein crystal structures", Macromolecules, Vol. 18, 1985, pp. 534-552.
16. Yue, K., Dill, K. A., "Forces of tertiary structural organization of globular proteins," Proc. Natl. Acad. Sci. USA, Vol. 92, 1995, pp. 146-150.
17. Lau K. F., Dill K. A., "A lattice statistical mechanics model of the conformational and sequence spaces of proteins", Macromoleculs, Vol. 22, 1989, pp. 3986-3997.
18. Li, H., Helling, R., Tang, C. and Wingreen, N., "Emergence of preferred structures in a simple model of protein folding," Science, Vol. 273, 1996, pp. 666-669.
19. Yin, L. and Ananthasuresh, G.K., "Topology Optimization of Compliant Mechanisms with Multiple Materials Using a Peak Function Material Interpolation Scheme," Structural and Multidisciplinary Optimization, Vol. 23, No. 1, 2001, pp. 49-62.
20. Yin, L. and Ananthasuresh, G.K., "Novel Design Technique for Electro-Thermally Actuated Compliant Micromechanisms," Sensors and Actuators, A Physical, Vol. 97-98, 2002, pp. 599-609.
21. Bendsøe, M. P., "Optimal shape design as a material distribution problem," Struct. Optim., Vol. 1, 1989, pp. 193-202.
22. Bendsøe, M. P. and Sigmund, O., "Material interpolation scheme in topology optimization," Arch. Appl. Mech., Vol. 69, 1999, pp. 635-654.
23. Rozvany, G. I. N., "Aims, scope, methods, history and unified terminology of computer-aided topology optimization in structural mechanis," Struct. Multidisc. Optim., Vol. 21, 2001, pp. 90-108.
24. rd ed, Wiley, John & Sons, 1996.
25. Lo, Chihsiung and Papalambros, P. Y., "A deterministic global design optimization method for nonconvex generalized polynomial problems," Journal of Mechanical Design, Vol. 118, 1996, pp. 75-81.
26. Lo, Chihsiung and Papalambros, P. Y., "A convex cutting plane algorithm for global solution of generalized polynomial optimal design models," Journal of Mechanical Design, Vol. 118, 1996, pp. 82-88.
27. Lo, Chihsiung and Papalambros, P. Y., "On global feasible search for global design optimization with application to generalized polynomial models," Journal of Mechanical Design, Vol. 117, 1995, pp. 402-408.
28. rd ed, Springer-Verlag New York, 1996.
29. Matlab, Numerical Analysis Software from Mathworks, Inc., Woburn, MA, USA., 2004, www.mathworks.com.
30. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, Vol. 28, 2001, pp. 235-242.