An enhanced version of SMMP-open-source software package for simulation of proteins

被引：45

作者：

Eisenmenger, F

Hansmann, UHE

Hayryan, S

Hu, CK ^{[1
]}

机构：

[1] Forschungsinst Mol Pharmakol, D-13125 Berlin, Germany

[2] Michigan Technol Univ, Houghton, MI 49931 USA

[3] Acad Sinica, Inst Phys, Taipei 11529, Taiwan

来源：

COMPUTER PHYSICS COMMUNICATIONS | 2006年 / 174卷 / 05期

基金：

美国国家科学基金会;

关键词：

FORTRAN package; protein folding; Monte Carlo; minimization; generalized-ensemble siniulations; structure prediction;

D O I：

10.1016/j.cpc.2005.10.013

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

We describe a revised and updated version of the program package SMMP (Simple Molecular Mechanics for Proteins) [F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192-212]. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. This announcement describes the first major revision of this software package and its newly added features.

引用

收藏

页码：422 / 429

页数：8

相关论文

共 18 条

[1] ICM - A NEW METHOD FOR PROTEIN MODELING AND DESIGN - APPLICATIONS TO DOCKING AND STRUCTURE PREDICTION FROM THE DISTORTED NATIVE CONFORMATION [J].

ABAGYAN, R ;

TOTROV, M ;

KUZNETSOV, D .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1994, 15 (05) :488-506

[2] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[3] 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

[4] ARVO:: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations [J].

Busa, J ;

Dzurina, J ;

Hayryan, E ;

Hayryan, S ;

Hu, CK ;

Plavka, J ;

Pokorny, I ;

Skrivánek, J ;

Wu, MC .

COMPUTER PHYSICS COMMUNICATIONS, 2005, 165 (01) :59-96

[5] 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

[6] [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

[7] Characteristic temperatures of folding of a small peptide [J].

Hansmann, UHE ;

Masuya, M ;

Okamoto, Y .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (20) :10652-10656

[8] A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients [J].

Hayryan, S ;

Hu, CK ;

Skrivánek, J ;

Hayryan, E ;

Pokorny, I .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (04) :334-343

[9]

MASUYA M, NOSL NUMERICAL CALCU

[10] SATISFYING HYDROGEN-BONDING POTENTIAL IN PROTEINS [J].

MCDONALD, IK ;

THORNTON, JM .

JOURNAL OF MOLECULAR BIOLOGY, 1994, 238 (05) :777-793