Effective computational reuse for energy evaluations in protein folding

Eunice E. Santos, Eugene Santos

Research output: Contribution to journalArticlepeer-review

Abstract

Predicting native conformations using computational protein models requires a large number of energy evaluations even with simplified models such as hydrophobichydrophilic (HP) models. Clearly, energy evaluations constitute a significant portion of computational time. We hypothesize that given the structured nature of algorithms that search for candidate conformations such as stochastic methods, energy evaluation computations can be cached and reused, thus saving computational time and effort. In this paper, we present a caching approach and apply it to 2D triangular HP lattice model. We provide theoretical analysis and prediction of the expected savings from caching as applied this model. We conduct experiments using a sophisticated evolutionary algorithm that contains elements of local search, memetic algorithms, diversity replacement, etc. in order to verify our hypothesis and demonstrate a significant level of savings in computational effort and time that caching can provide.

Original languageEnglish (US)
Pages (from-to)725-739
Number of pages15
JournalInternational Journal on Artificial Intelligence Tools
Volume15
Issue number5
DOIs
StatePublished - Oct 1 2006
Externally publishedYes

Keywords

  • Caching
  • Evolutionary algorithms
  • HP energy model
  • Protein folding
  • Reuse
  • Triangular lattice

ASJC Scopus subject areas

  • Artificial Intelligence

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