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Challenges of continuous global optimization in molecular structure prediction

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journal contribution
posted on 2007-09-16, 00:00 authored by Gleb BeliakovGleb Beliakov, Kieran LimKieran Lim
The molecular geometry, the three dimensional arrangement of atoms in space, is a major factor determining the properties and reactivity of molecules, biomolecules and macromolecules. Computation of stable molecular conformations can be done by locating minima on the potential energy surface (PES). This is a very challenging global optimization problem because of extremely large numbers of shallow local minima and complicated landscape of PES. This paper illustrates the mathematical and computational challenges on one important instance of the problem, computation of molecular geometry of oligopeptides, and proposes the use of the Extended Cutting Angle Method (ECAM) to solve this problem.

ECAM is a deterministic global optimization technique, which computes tight lower bounds on the values of the objective function and fathoms those part of the domain where the global minimum cannot reside. As with any domain partitioning scheme, its challenge is an extremely large partition of the domain required for accurate lower bounds. We address this challenge by providing an efficient combinatorial algorithm for calculating the lower bounds, and by combining ECAM with a local optimization method, while preserving the deterministic character of ECAM.


History

Journal

European journal of operational research

Volume

181

Pagination

1198 - 1213

Location

Amsterdam, The Netherlands

Open access

  • Yes

ISSN

0377-2217

eISSN

1872-6860

Language

eng

Publication classification

C1 Refereed article in a scholarly journal

Copyright notice

2006, Elsevier B.V.