A New Monte Carlo Algorithm for Protein Folding

Abstract

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for lattice heteropolymers, and compare to published Monte Carlo studies. In all cases our algorithms are faster than all previous ones, and in several cases we find new minimal energy states. In addition to ground states, our algorithms give estimates for the partition sum at finite temperatures.

4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett., revised version with changes in the text

References in corpus (3)

• Phase Transitions of Single Semi-stiff Polymer Chains
• Long Range Moves for High Density Polymer Simulations
• Critical Unmixing of Polymer Solutions

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• Optimized Wang-Landau sampling of lattice polymers: Ground state search and folding thermodynamics of HP model proteins
• Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins
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• Exact Sequence Analysis for Three-Dimensional HP Lattice Proteins
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• Exactness of the Annealed and the Replica Symmetric Approximations for Random Heteropolymers
• Four-dimensional polymer collapse II: Interacting self-avoiding trails
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• Monte Carlo Investigation of Lattice Models of Polymer Collapse in Five Dimensions
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