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Monte Carlo Procedure for Protein Design

Anders Irbäck·Carsten Peterson·Frank Potthast·Erik Sandelin
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Abstract

A new method for sequence optimization in protein models is presented. The approach, which has inherited its basic philosophy from recent work by Deutsch and Kurosky [Phys. Rev. Lett. 76, 323 (1996)] by maximizing conditional probabilities rather than minimizing energy functions, is based upon a novel and very efficient multisequence Monte Carlo scheme. By construction, the method ensures that the designed sequences represent good folders thermodynamically. A bootstrap procedure for the sequence space search is devised making very large chains feasible. The algorithm is successfully explored on the two-dimensional HP model with chain lengths N=16, 18 and 32.

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Anders Irbäck, Carsten Peterson, Frank Potthast, Erik Sandelin. 1998-09-19. Monte Carlo Procedure for Protein Design. https://doi.org/10.1103/physreve.58.r5249

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