Parallel tempering simulations of HP-36

被引：85

作者：

Lin, CY

Hu, CK

Hansmann, UHE ^{[1
]}

机构：

[1] Michigan Technol Univ, Dept Phys, Houghton, MI 49931 USA

[2] Acad Sinica, Inst Phys, Taipei 115, Taiwan

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2003年 / 52卷 / 03期

关键词：

protein-folding problem; structure prediction; Monte Carlo simulation; implicit solvent;

D O I：

10.1002/prot.10351

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We report results from all-atom Monte Carlo simulations of the 36-residue villin headpiece subdomain HP-36. Protein-solvent interactions are approximated by an implicit solvent model. The parallel tempering is used to overcome the problem of slow convergence in low-temperature protein simulations. Our results show that this technique allows one to sample native-like structures of small proteins and points out the need for improved energy functions. (C) 2003Wiley-Liss, Inc.

引用

收藏

页码：436 / 445

页数：10

相关论文

共 18 条

[1] Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution [J].

Duan, Y ;

Kollman, PA .

SCIENCE, 1998, 282 (5389) :740-744

[2] THE DOUBLE CUBIC LATTICE METHOD - EFFICIENT APPROACHES TO NUMERICAL-INTEGRATION OF SURFACE-AREA AND VOLUME AND TO DOT SURFACE CONTOURING OF MOLECULAR ASSEMBLIES [J].

EISENHABER, F ;

LIJNZAAD, P ;

ARGOS, P ;

SANDER, C ;

SCHARF, M .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1995, 16 (03) :273-284

[3] [SMMP] A modern package for simulation of proteins [J].

Eisenmenger, F ;

Hansmann, UHE ;

Hayryan, S ;

Hu, CK .

COMPUTER PHYSICS COMMUNICATIONS, 2001, 138 (02) :192-212

[4] Folding of a small helical protein using hydrogen bonds and hydrophobicity forces [J].

Favrin, G ;

Irbäck, A ;

Wallin, S .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2002, 47 (02) :99-105

[5] Parallel tempering algorithm for conformational studies of biological molecules [J].

Hansmann, UHE .

CHEMICAL PHYSICS LETTERS, 1997, 281 (1-3) :140-150

[6] PREDICTION OF PEPTIDE CONFORMATION BY MULTICANONICAL ALGORITHM - NEW APPROACH TO THE MULTIPLE-MINIMA PROBLEM [J].

HANSMANN, UHE ;

OKAMOTO, Y .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1993, 14 (11) :1333-1338

[7] Global optimization by energy landscape paving [J].

Hansmann, UHE ;

Wille, LT .

PHYSICAL REVIEW LETTERS, 2002, 88 (06) :68105/1-68105/4

[8] New Monte Carlo algorithms for protein folding [J].

Hansmann, UHE ;

Okamoto, Y .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 1999, 9 (02) :177-183

[9]

HANSMANN UHE, 1998, ANN REV COMPUTATIONA

[10]

HUKUSHIMA K, 1995, J AM STAT ASSOC, V90, P909