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Challenges of continuous global optimization in molecular structure prediction
Authors:Gleb Beliakov  Kieran F Lim
Institution:Faculty of Science and Technology, Deakin University, 221 Burwood Hwy, Burwood 3125, Australia
Abstract: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.
Keywords:Global optimization  Nonlinear programming  Molecular conformation  Branch and bound  Computational chemistry
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