Teaching computers to fold proteins

被引：10

作者：

Winther, O ^{[1
]}

Krogh, A ^{[1
]}

机构：

[1] Tech Univ Denmark, Ctr Biol Sequence Anal, DK-2800 Lyngby, Denmark

来源：

PHYSICAL REVIEW E | 2004年 / 70卷 / 03期

关键词：

D O I：

10.1103/PhysRevE.70.030903

中图分类号：

O35 [流体力学]; O53 [等离子体物理学];

学科分类号：

070204 ; 080103 ; 080704 ;

摘要：

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Lennard-Jones (LJ) force field with a torsional angle degrees-of-freedom and a single-atom side-chain. In a test with 24 peptides of known structure, none folded correctly with the initial potential functions, but two-thirds came within 3 Angstrom to their native fold after optimizing the potential functions.

引用

页数：4

共 25 条

[1] PRINCIPLES THAT GOVERN FOLDING OF PROTEIN CHAINS [J].

ANFINSEN, CB .

SCIENCE, 1973, 181 (4096) :223-230

[2] How to guarantee optimal stability for most representative structures in the protein data bank [J].

Bastolla, U ;

Farwer, J ;

Knapp, EW ;

Vendruscolo, M .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 2001, 44 (02) :79-96

[3] A statistical mechanical method to optimize energy functions for protein folding [J].

Bastolla, U ;

Vendruscolo, M ;

Knapp, EW .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (08) :3977-3981

[4]

Bonneau R, 2001, PROTEINS, P119

[5] CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].

BROOKS, BR ;

BRUCCOLERI, RE ;

OLAFSON, BD ;

STATES, DJ ;

SWAMINATHAN, S ;

KARPLUS, M .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217

[6] ANNEALING MARKOV-CHAIN MONTE-CARLO WITH APPLICATIONS TO ANCESTRAL INFERENCE [J].

GEYER, CJ ;

THOMPSON, EA .

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 1995, 90 (431) :909-920

[7] OPTIMAL PROTEIN-FOLDING CODES FROM SPIN-GLASS THEORY [J].

GOLDSTEIN, RA ;

LUTHEYSCHULTEN, ZA ;

WOLYNES, PG .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1992, 89 (11) :4918-4922

[8] How optimization of potential functions affects protein folding [J].

Hao, MH ;

Scheraga, HA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1996, 93 (10) :4984-4989

[9]

Hinton G. E., 1983, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, P448

[10] Three-helix-bundle protein in a Ramachandran model [J].

Irbäck, A ;

Sjunnesson, F ;

Wallin, S .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (25) :13614-13618

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