Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules
Joint Authors
Molloy, Kevin
Hashmi, Irina
Olson, Brian
Shehu, Amarda
Source
Advances in Artificial Intelligence
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-19, 19 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-12-04
Country of Publication
Egypt
No. of Pages
19
Main Subjects
Information Technology and Computer Science
Science
Abstract EN
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.
American Psychological Association (APA)
Olson, Brian& Hashmi, Irina& Molloy, Kevin& Shehu, Amarda. 2012. Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules. Advances in Artificial Intelligence،Vol. 2012, no. 2012, pp.1-19.
https://search.emarefa.net/detail/BIM-489535
Modern Language Association (MLA)
Olson, Brian…[et al.]. Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules. Advances in Artificial Intelligence No. 2012 (2012), pp.1-19.
https://search.emarefa.net/detail/BIM-489535
American Medical Association (AMA)
Olson, Brian& Hashmi, Irina& Molloy, Kevin& Shehu, Amarda. Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules. Advances in Artificial Intelligence. 2012. Vol. 2012, no. 2012, pp.1-19.
https://search.emarefa.net/detail/BIM-489535
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-489535