Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules. (4th December 2012)

• Record Type: Journal Article
• Authors: Olson, Brian; Hashmi, Irina; Molloy, Kevin; Shehu, Amarda
• Other Names: Luo Zhiyuan Academic Editor.
• Is Part Of: Advances in artificial intelligence. Volume 2012(2012)
• Publication Date: 2012-12-04
• Subjects: Artificial intelligence -- Periodicals; Artificial intelligence; Periodicals; Electronic journals; 006.3
• DOI: 10.1155/2012/674832
• Languages: English
• ISSNs: 1687-7470

Abstract

Abstract : Since its introduction, the basin hopping (BH) framework has proven useful for hard nonlinear optimization problems with multiple variables and modalities. Applications span a wide range, from packing problems in geometry to characterization of molecular states in statistical physics. BH is seeing a reemergence in computational structural biology due to its ability to obtain a coarse-grained representation of the protein energy surface in terms of local minima. In this paper, we show that the BH framework is general and versatile, allowing to address problems related to the characterization of protein structure, assembly, and motion due to its fundamental ability to sample minima in a high-dimensional variable space. We show how specific implementations of the main components in BH yield algorithmic realizations that attain state-of-the-art results in the context of ab initio protein structure prediction and rigid protein-protein docking. We also show that BH can map intermediate minima related with motions connecting diverse stable functionally relevant states in a protein molecule, thus serving as a first step towards the characterization of transition trajectories connecting these states.