Anders Irbäck, Carsten Peterson, Frank Potthast and Erik Sandelin
Monte Carlo Procedure for Protein Design
Physical Review E 58, R5249-R5252 (1998)

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.

LU TP 97-33