TACKLING THE MULTIPLE-MINIMA PROBLEM IN PROTEIN FOLDING BY MONTE CARLO SIMULATED ANNEALING AND GENERALIZED-ENSEMBLE ALGORITHMS

Yuko Okamoto ()
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Yuko Okamoto: Dept. of Theoretical Studies, Institute for Molecular Science, Dept. of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan

International Journal of Modern Physics C (IJMPC), 1999, vol. 10, issue 08, 1571-1582

Abstract: Monte Carlo simulations based on simulated annealing and multicanonical algorithm have been performed to predict the secondary and tertiary structures of oligopeptide systems. Two oligopeptides, C-peptide of ribonuclease A and the fragment BPTI(16-36) of bovine pancreatic trypsin inhibitor, were studied. Only the amino-acid sequence information was used as input and initial conformations were randomly generated. The lowest-energy conformations obtained haveα-helix structure andβ-sheet structure for C-peptide and BPTI(16-36), respectively, in remarkable agreement with experimental results.

Keywords: Simulated annealing; Generalized-ensemble algorithms; Multicanonical algorithm; Replica-exchange method; Parallel tempering; Simulated tempering (search for similar items in EconPapers)
Date: 1999
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DOI: 10.1142/S0129183199001352

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