Local minima-based exploration for off-lattice protein folding

E. S. Keum, K. J. Kim, E. E. Santos

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We present a new and simple algorithmic approach to help predict protein structures from amino acid sequences based on energy minimization. In the search for the minimal energy conformation, we analyze and exploit the protein structures found at the various local minima to direct the search the global minimum. As such, we explore the energy landscape efficiently by considering only the space of local minima instead of the whole feasible space of conformations. Our specific algorithmic approach is comprised of two different elements: local minimization and operators from genetic algorithms. Unlike existing hybrid approaches where the local optimization is used to fine-tune the solutions, we focus primarily on the local optimization and employ stochastic sampling through genetic operators for diversification. Our empirical results indicate that each local minimum is representative of the substructures contained in the set of solutions surrounding the local minima. We applied our approach to determining the minimal energy conformation of proteins from the protein data bank (PDB) using the CHARMM and UNRES energy model. We compared against standard genetic algorithms and Monte Carlo approaches as well as the conformations found in the PDB as the baseline. In all cases, our new approach computed the lowest energy conformation.

Original languageEnglish (US)
Title of host publicationProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages615-616
Number of pages2
ISBN (Electronic)0769520006, 9780769520001
DOIs
StatePublished - Jan 1 2003
Externally publishedYes
Event2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States
Duration: Aug 11 2003Aug 14 2003

Publication series

NameProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Other

Other2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
CountryUnited States
CityStanford
Period8/11/038/14/03

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Science Applications

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