Iterative convex quadratic approximation for global optimization in protein docking

Computational Optimization and Applications

Volumn 32, Issue 3, 2005, Pages 285-297

  Marcia, Roummel F ^a   Mitchell, Julie C ^a   Rosen, J Ben ^b  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Convex underestimator; Docking mesh evaluator; Global optimization; Potential energy; Protein docking

Indexed keywords

CONVEX UNDERESTIMATOR; DOCKING MESH EVALUATOR; PROTEIN DOCKING;

APPROXIMATION THEORY; CONVERGENCE OF NUMERICAL METHODS; FUNCTIONS; ITERATIVE METHODS; POTENTIAL ENERGY; PROTEINS; QUADRATIC PROGRAMMING;

GLOBAL OPTIMIZATION;

EID: 26044460229     PISSN: 09266003     EISSN: 15732894     Source Type: Journal    
DOI: 10.1007/s10589-005-4799-4     Document Type: Article

References (12)

1. N. Baker, M. Holst, and F. Wang, "Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II: Refinement at solvent accessible surfaces in biomolecular systems," J. Comput. Chem., vol. 21, pp. 1343-1352, 2000.
2. K.A. Dill, A.T. Phillips, and J.B. Rosen, CGU: An algorithm for molecular structure prediction, in Large-scale optimization with applications, Part III (Minneapolis, MN, 1995), vol. 94 of IMA Vol. Math. Appl., Springer: New York, 1997, pp. 1-21.
3. P.E. Gill, W. Murray, M.A. Saunders, and M.H. Wright, "User's guide for NPSOL (version 4.0): A Fortran package for nonlinear programming," Tech. Rep. SOL-86-2, Systems Optimization Laboratory, Stanford University, Stanford, CA, 1986.
4. D.S. Goodsell and A.J. Olson, "Automated docking of substrates to proteins by simulated annealing," Proteins: Struct. Fun. Gen., vol. 8, pp. 195-202, 1990.
5. M. Holst, N. Baker, and F. Wang, "Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: Algorithms and examples," J. Comput. Chem., vol. 21, pp. 1319-1342, 2000.
6. R. Hooke and T. A. Jeeves, "Direct search solution of numerical and statistical problems," J. Assoc. Comput. Mach., vol. 8, pp. 212-229, 1961.
7. J. Janin, "Welcome to CAPRI: A critical assessment of predicted interactions," Proteins: Struct. Func. Genet., vol. 47, no. 3, p. 257, 2002.
8. E.C. Meng, B.K. Shoichet, and I.D. Kuntz, "Automated docking with grid-based energy evaluation," J. Comp. Chem., vol. 13, pp. 505-524, 1992.
9. J.C. Mitchell, J.B. Rosen, A.T. Phillips, and L.F. Ten Eyck, "Coupled optimization in protein docking," in Proceedings of the Third Annual International Conference on Computational Molecular Biology, ACM Press, 1999, pp. 280-284.
10. J.B. Rosen, K.A. Dill, and A.T. Phillips, "Protein structure and energy landscape dependence on sequence using a continuous energy function," J. Comp. Biol., vol. 4, pp. 227-239, 1997.
11. J.B. Rosen and R.F. Marcia, "Convex quadratic approximation," Comput. Optim. Appl., vol. 28, pp. 173-184, 2004.
12. 1 norm minimization," Comput. Optim. Appl., vol. 17, pp. 329-341, 2000.