Monte Carlo procedure for protein design
(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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https://lup.lub.lu.se/record/11309f21-d2c2-41fb-bdea-20ad90df2b5c
- author
- Irbäck, Anders LU ; Peterson, Carsten LU ; Potthast, Frank LU and Sandelin, Erik LU
- organization
- publishing date
- 1998
- 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
- 2024-02-19 01:47:25
@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}}, }