A semi-definite programming-based underestimation method for global optimization in molecular docking

Proceedings of the 44th IEEE Conference on Decision and Control, and the European Control Conference, CDC-ECC '05

Volumn 2005, Issue , 2005, Pages 3675-3680

  Paschalidis, Ioannis Ch ^a,b   Shen, Yang ^b   Vajda, Sandor ^b   Vakili, Pirooz ^a,b  

^a IEEE   (United States)

^b Boston University   (United States)

Author keywords

Computational biology; Global optimization; Molecular docking; Semi definite programming

Indexed keywords

COMPUTATIONAL BIOLOGY; CONVEX GLOBAL UNDERESTIMATOR (CGU); MOLECULAR DOCKING; SEMI-DEFINITE PROGRAMMING;

BINDING ENERGY; FUNCTION EVALUATION; MOLECULAR DYNAMICS; PROBLEM SOLVING; PROTEINS;

GLOBAL OPTIMIZATION;

EID: 33847230554     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CDC.2005.1582733     Document Type: Conference Paper

References (9)

1. C. Levinthal, "Are there pathways for protein folding?" J. Chim. Phys., vol. 65, pp. 44-45, 1968.
2. C. J. Camacho, Z. Weng, S. Vajda, and C. DeLisi, "Free energy land-scapes of encounter complexes in protein-protein association," Biophys. J., vol. 76, pp. 1166-1178, 1999.
3. S. Dennis and S. Vajda, 'Semi-global simplex optimization and its application to determining the preferred solvation sites of proteins," J. Comp. Chem., vol. 23, no. 3, pp. 319-334, 2002.
4. C. Camacho and S. Vajda, "Protein docking along smooth association pathways," Proc. Natl. Acad. Sci. USA, vol. 98, pp. 10636-10641, 2001.
5. A. Phillips, J. Rosen, and K. Dill, From Local to Global Optimization (P.M. Pardalos et al, Eds.). Kluwer Academic Publishers, 2001, ch. Convex Global Underestimation for Molecular Structure Prediction, pp. 1-18.
6. S. Vajda, M. Sippl, and J. Novotny, "Empirical potentials and functions for protein folding and binding," Curr. Op. Struct. Biol., vol. 7, pp. 222-228, 1997.
7. A. Ben-Tal and A. Nemirovski, Lectures on Modern Convex Optimization. SIAM, 2001.
8. J. Rosen and R. Marcia, 'Convex quadratic approximation," Computational Optimization and Applications, vol. 28, pp. 173-184, 2004.
9. R. Hettich and K. O. Kortanek, "Semi-infi nite programming: theory, methods and applications," SIAM Review, vol. 35, no. 3, pp. 380-429, 1993.