Wordom: a program for efficient analysis of molecular dynamics simulations

被引：235

作者：

Seeber, Michele ^{[1
]}

Cecchini, Marco ^{[1
]}

Rao, Francesco ^{[1
]}

Settanni, Giovanni ^{[1
]}

Caflisch, Amedeo ^{[1
]}

机构：

[1] Univ Zurich, Dept Biochem, CH-8057 Zurich, Switzerland

来源：

BIOINFORMATICS | 2007年 / 23卷 / 19期

关键词：

D O I：

10.1093/bioinformatics/btm378

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Wordom is a versatile program for manipulation of molecular dynamics trajectories and efficient analysis of simulations. Original tools in Wordom include a procedure to evaluate significance of sampling for principal component analysis as well as modules for clustering multiple conformations and evaluation of order parameters for folding and aggregation. The program was developed with special emphasis on user-friendliness, effortless addition of new modules and efficient handling of large sets of trajectories.

引用

页码：2625 / 2627

页数：3

共 17 条

[1] ESSENTIAL DYNAMICS OF PROTEINS [J].

AMADEI, A ;

LINSSEN, ABM ;

BERENDSEN, HJC .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1993, 17 (04) :412-425

[2] On the calculation of entropy from covariance matrices of the atomic fluctuations [J].

Andricioaei, I ;

Karplus, M .

JOURNAL OF CHEMICAL PHYSICS, 2001, 115 (14) :6289-6292

[3]

[Anonymous], 1975, CLUSTERING ALGORITHM

[4] 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

[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] Replica exchange molecular dynamics simulations of amyloid peptide aggregation [J].

Cecchini, M ;

Rao, F ;

Seeber, M ;

Caflisch, A .

JOURNAL OF CHEMICAL PHYSICS, 2004, 121 (21) :10748-10756

[7]

Chan HS, 1998, PROTEINS, V30, P2, DOI 10.1002/(SICI)1097-0134(19980101)30:1<2::AID-PROT2>3.0.CO

[8]

2-R

[9]

DeLano WL, 2002, PYMOL MOL GRAPHICS S, DOI DOI 10.1021/bi801610c

[10] Exploring expression data: Identification and analysis of coexpressed genes [J].

Heyer, LJ ;

Kruglyak, S ;

Yooseph, S .

GENOME RESEARCH, 1999, 9 (11) :1106-1115

← 1 2 →