Monte Carlo Procedure for Protein Design
Soft Condensed Matter
2009-10-30 v3 Disordered Systems and Neural Networks
High Energy Physics - Lattice
Chemical Physics
Biomolecules
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.
Cite
@article{arxiv.cond-mat/9711092,
title = {Monte Carlo Procedure for Protein Design},
author = {Anders Irbäck and Carsten Peterson and Frank Potthast and Erik Sandelin},
journal= {arXiv preprint arXiv:cond-mat/9711092},
year = {2009}
}
Comments
7 pages LaTeX, 4 Postscript figures; minor changes