Basin Hopping

One of our first algorithms, PLOW, built on the Basin Hopping framework, known as the Iterative Local Sampling method in evolutionary computing. A series of local search and perturbation operations allow PLOW to hop between local minima in the conformational space. PLOW was shown both effective and comparable to other state-of-the-art conformational search algorithms in terms of the quality of the decoy ensemble generated. This work has appeared in: 1) Brian Olson and Amarda Shehu. "Evolutionary-inspired Probabilistic Search for Enhancing Sampling of Local Minima in the Protein Energy Surface." Proteome Science 2012, 10(Suppl1): S5; and 2) Brian Olson and Amarda Shehu. "Populating Local Minima in the Protein Conformational Space." IEEE Intl Conf on Bioinf and Biomed (IEEE BIBM), Atlanta, GA, 2011, pg. 114-117.

Detailed analysis of the method has shown that its ability to preserve adjacency between local minima is strongly correlated to its ability to approach the protein native state. This work has appeared in: 3) Brian Olson and Amarda Shehu. "Efficient Basin Hopping in the Protein Energy Surface." IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), pg. 119-124, Philadelphia, PA, 2012. An extended version of this work is in: 4) Brian Olson and Amarda Shehu. "Rapid Sampling of Local Minima in Protein Energy Surface and Effective Reduction through a Multi-objective Filter." Proteome Science, 2013.

We have shown recently that, indeed, Basin Hopping is an effective framework that can be generally applied for conformational search, whether in modeling one protein chain or a dimeric assembly of two protein chains, or even in mapping potentially transition-relevant regions in the energy surface around two given functional states of a protein system. This work has appeared in: 5) Brian Olson, Irina Hashmi, Kevin Molloy, and Amarda Shehu. Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules. Advances in Artificial Intelligence J 2012, 674832 (special issue on Artificial Intelligence Applications in Biomedicine). Additional realizations of Basin Hopping for protein-protein docking have been pursued and can be found under description of docking research in our lab.

On this Project:

  • Brian Olson

    Sameh Saleh (Undergraduate Student)

    Irina Hashmi

    Kenneth De Jong

    Amarda Shehu

This material is based upon work supported by the National Science Foundation under Grant No. 1016995 and IIS CAREER Award No. 1144106. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.