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Challenges of continuous global optimization in molecular structure prediction

Beliakov, Gleb and Lim, Kieran 2007, Challenges of continuous global optimization in molecular structure prediction, European journal of operational research, vol. 181, no. 3, pp. 1198-1213.

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Title Challenges of continuous global optimization in molecular structure prediction
Author(s) Beliakov, Gleb
Lim, Kieran
Journal name European journal of operational research
Volume number 181
Issue number 3
Start page 1198
End page 1213
Publisher Elsevier BV
Place of publication Amsterdam, The Netherlands
Publication date 2007-09-16
ISSN 0377-2217
1872-6860
Keyword(s) global optimization
nonlinear programming
molecular conformation
branch and bound
computational chemistry
Summary 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.


Language eng
Field of Research 010303 Optimisation
HERDC Research category C1 Refereed article in a scholarly journal
Copyright notice ©2006, Elsevier B.V.
Persistent URL http://hdl.handle.net/10536/DRO/DU:30007158

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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.