Challenges of continuous global optimization in molecular structure prediction

European Journal of Operational Research

Volumn 181, Issue 3, 2007, Pages 1198-1213

  Beliakov, Gleb ^a   Lim, Kieran F ^a  

^a DEAKIN UNIVERSITY   (Australia)

Author keywords

Branch and bound; Computational chemistry; Global optimization; Molecular conformation; Nonlinear programming

Indexed keywords

BIOMOLECULES; COMPUTATIONAL GEOMETRY; CONFORMATIONS; MACROMOLECULES; MOLECULAR STRUCTURE; NONLINEAR PROGRAMMING; PEPTIDES;

BRANCH AND BOUND; COMPUTATIONAL CHEMISTRY; MOLECULAR CONFORMATION; MOLECULAR GEOMETRY;

GLOBAL OPTIMIZATION;

EID: 33947629307     PISSN: 03772217     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejor.2005.08.033     Document Type: Article

References (38)

1. Andramonov M., Rubinov A., and Glover B. Cutting angle methods in global optimization. Applied Mathematics Letters 12 3 (1999) 95-100
2. Aurenhammer F. Voronoi diagrams - a survey of a fundamental data structure. ACM Computing Surveys 23 (1991) 345-405
3. Banks W.A., Kastin A.J., and Michals E.A. Tyr-mif-1 and met-enkephalin share a saturable blood-brain barrier transport system. Peptides 8 (1987) 899-903
4. Batten L., and Beliakov G. Fast algorithm for the cutting angle method of global optimization. Journal of Global Optimization 24 (2002) 149-161
5. Beliakov G., Ting K.M., Murshed M., Rubinov A., and Bertoli M. Efficient serial and parallel implementations of the cutting angle method. In: Di Pillo G. (Ed). High Performance Algorithms and Software for Nonlinear Optimization (2003), Kluwer Academic Publishers 57-74
6. Beliakov G. Geometry and combinatorics of the cutting angle method. Optimization 52 (2003) 379-394
7. Beliakov G. The cutting angle method - a tool for constrained global optimization. Optimization Methods and Software 19 (2004) 137-151
8. G. Beliakov, Extended cutting angle method of constrained global optimization, in: L. Caccetta (Ed.), Optimization in Industry, Springer, Heidelberg, in press.
9. Bihari B., and Plotnikoff N. Methionine enkephalin in the treatment of aids-related complex. In: Plotnikoff N., Mugo A., Faith E., and Good R.A. (Eds). Cytokines: Stress and Immunity (1999), CRC Press, Boca Raton (FL)
10. Board on Chemical Sciences and Technology, Beyond the Molecular Frontier: Challenges for Chemistry and Chemical Engineering, National Academies Press, Washington (DC), 2003.
11. Boissonnat J.-D., Sharir M., Tagansky B., and Yvinec M. Voronoi diagrams in higher dimensions under certain polyhedral distance functions. Discrete and Computational Geometry 19 (1998) 485-519
12. Eksterowicz J., and Houk K. Transition state modeling with empirical force fields. Chemical Reviews 93 7 (1993) 2439-2461
13. In: Cohen N. (Ed). Guidebook on Molecular Modeling in Drug Design (1996), Academic Press, San Diego
14. Demyanov V., and Rubinov A. Constructive Nonsmooth Analysis (1995), Peter Lang, Frankfurt am Main
15. Floudas C.A. Deterministic Global Optimization: Theory, Methods, and Applications. Nonconvex Optimization and its Applications vol. 37 (2000), Kluwer Academic Publishers, Dordrecht, London
16. Hansen P., and Jaumard B. Lipschitz optimization. In: Horst R., and Pardalos P. (Eds). Handbook of Global Optimization (1995), Kluwer, Dordrecht 407-493
17. Horst R., and Tuy H. Global Optimization: Deterministic Approaches. second ed. (1993), Springer-Verlag, Berlin, New York
18. Horst R., and Pardalos P.M. Handbook of Global Optimization. Nonconvex Optimization and its Applications vol. 2 (1995), Kluwer Academic Publishers, Dordrecht, Boston
19. Horst R., Pardalos P., and Thoai N. Introduction to Global Optimization. second ed. (2000), Kluwer Academic Publishers, Dordrecht
20. Hughes J., Smith T., Kosterlitz H., Fothergill L., Morgan B., and Morris H. Identification of two related pentapeptides from the brain with potent opiate agonist activity. Nature 258 (1975) 577-580
21. Klepeis J.L., Ierapetritou M.G., and Floudas C.A. Protein folding and peptide docking - a molecular modeling and global optimization approach. Computers and Chemical Engineering 22 Suppl S (1998) S3-S10
22. Leach A. Molecular Modelling: Principles and Applications (1996), Addison-Wesley, Longman, Harlow (UK)
23. Lim K., Beliakov G., and Batten L. Predicting molecular structures: Application of the cutting angle method. Physical Chemistry Chemical Physics 5 (2003) 3884-3890
24. Muegge I., and Rarey M. Small molecule docking and scoring. In: Lipkowitz K., and Boyd D. (Eds). Reviews in Computational Chemistry vol. 17 (2001), Wiley-VCH, New York 1-60
25. Nayeem A., Vila J., and Scheraga H. A comparative study of the simulated annealing and Monte Carlo with minimization approaches to the minimum energy structures of polypeptides: Met-enkephalin. Journal of Computational Chemistry 12 (1991) 594-605
26. Némethy G., Gibson K., Palmer K., Yoon C., Paterlini G., Zagari A., Rumsey S., and Scheraga H. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ecepp/3 algorithm, with application to proline-containing peptides. Journal of Physical Chemistry 96 15 (1992) 6472-6484
27. Neumaier A. Molecular modeling of proteins and mathematical prediction of protein structure. SIAM Review 39 3 (1997) 407-460
28. Pallaschke D., and Rolewicz S. Foundations of Mathematical Optimization (1997), Kluwer Academic Publishers, Dordrecht
29. Pardalos P.M., and Floudas C.A. Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches (2000), Kluwer Academic Publishers, Boston
30. Pijavski S. An algorithm for finding the absolute extremum of a function. USSR Computational Mathematics and Mathematical Physics 2 (1972) 57-67
31. Pinter J. Global Optimization in Action: Continuous and Lipschitz Optimization-Algorithms, Implementations, and Applications. Nonconvex Optimization and its Applications vol. 6 (1996), Kluwer Academic Publishers, Dordrecht, Boston
32. Rubinov A. Abstract Convexity and Global Optimization. Nonconvex Optimization and its Applications vol. 44 (2000), Kluwer Academic Publishers, Dordrecht, Boston
33. Scheraga H. Predicting three-dimensional structure of oligopeptides. In: Lipkowitz K., and Boyd D. (Eds). Reviews in Computational Chemistry vol. 3 (1992), VCH Publishers, New York 73-142
34. Shubert B. A sequential method seeking the global maximum of a function. SIAM Journal of Numerical Analysis 9 (1972) 379-388
35. Strongin R.G., and Sergeyev Y.D. Global Optimization with Non-convex Constraints: Sequential and Parallel Algorithms. Nonconvex Optimization and its Applications vol. 45 (2000), Kluwer Academic, Dordrecht, London
36. Wales D.J., and Scheraga H.A. Review: Chemistry - global optimization of clusters, crystals, and biomolecules. Science 285 5432 (1999) 1368-1372
37. In: Webster D. (Ed). Protein Structure Prediction: Methods and Protocols (2000), Humana, Totowa (NJ)
38. Young D. Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems (2001), John Wiley and Sons