Monte Carlo procedure for protein design

Summary, in English

A 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 different 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 [K. F. Lau and K. A. Dill, Macromolecules 32, 3986 (1989)] with chain lengths N= 16, 18, and 32.

• Author: Anders Irbäck; Carsten Peterson; Frank Potthast; Erik Sandelin
• Department/s: Computational Biology and Biological Physics - Has been reorganised
• Publishing year: 1998
• Language: English
• Publication/Series: Physical Review E
• Volume: 58
• Issue: 5
• Links: http://dx.doi.org/10.1103/PhysRevE.58.R5249
• Document type: Journal article
• Publisher: American Physical Society
• Status: Published
• ISBN/ISSN/Other: ISSN: 1063-651X