Efficient conformational search method for peptides and proteins

Monte Carlo minimization with an adaptive bias

Sefika Ozkan, Hagai Meirovitch

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

The energy function of a protein consists of a tremendous number of minima. Locating the global energy minimum (GEM), which corresponds to the native structure, is a severe problem in global optimization. The commonly used Monte Carlo minimization (MCM) method is based on a random selection of torsional angle values. We suggest selecting these values with biased probabilities depending on the increased structure-energy correlations as the GEM is approached during the search. Our method applied to models of the 5-residue peptide Leu-enkephalin finds the GEM ∼2.7 faster than MCM.

Original languageEnglish (US)
Pages (from-to)9128-9131
Number of pages4
JournalJournal of Physical Chemistry B
Volume107
Issue number34
StatePublished - Aug 28 2003
Externally publishedYes

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Peptides
peptides
proteins
Proteins
Leucine Enkephalin
optimization
Global optimization
energy

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Efficient conformational search method for peptides and proteins : Monte Carlo minimization with an adaptive bias. / Ozkan, Sefika; Meirovitch, Hagai.

In: Journal of Physical Chemistry B, Vol. 107, No. 34, 28.08.2003, p. 9128-9131.

Research output: Contribution to journalArticle

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