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Monte Carlo procedure for protein design

Irbäck, Anders LU orcid ; Peterson, Carsten LU ; Potthast, Frank LU and Sandelin, Erik LU (1998) In Physical Review E 58(5).
Abstract

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.

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author
; ; and
organization
publishing date
type
Contribution to journal
publication status
published
in
Physical Review E
volume
58
issue
5
publisher
American Physical Society
external identifiers
  • scopus:0000781041
ISSN
1063-651X
DOI
10.1103/PhysRevE.58.R5249
language
English
LU publication?
yes
id
11309f21-d2c2-41fb-bdea-20ad90df2b5c
date added to LUP
2016-08-17 17:55:16
date last changed
2025-10-14 11:12:11
@article{11309f21-d2c2-41fb-bdea-20ad90df2b5c,
  abstract     = {{<p>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.</p>}},
  author       = {{Irbäck, Anders and Peterson, Carsten and Potthast, Frank and Sandelin, Erik}},
  issn         = {{1063-651X}},
  language     = {{eng}},
  number       = {{5}},
  publisher    = {{American Physical Society}},
  series       = {{Physical Review E}},
  title        = {{Monte Carlo procedure for protein design}},
  url          = {{http://dx.doi.org/10.1103/PhysRevE.58.R5249}},
  doi          = {{10.1103/PhysRevE.58.R5249}},
  volume       = {{58}},
  year         = {{1998}},
}