Literature DB >> 17717034

Wordom: a program for efficient analysis of molecular dynamics simulations.

Michele Seeber1, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch.   

Abstract

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.

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Year:  2007        PMID： 17717034     DOI： 10.1093/bioinformatics/btm378

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  83 in total

1.  A gain-of-function mutation of Arabidopsis cryptochrome1 promotes flowering.

Authors:  Vivien Exner; Cristina Alexandre; Gesa Rosenfeldt; Pietro Alfarano; Mena Nater; Amedeo Caflisch; Wilhelm Gruissem; Alfred Batschauer; Lars Hennig
Journal:  Plant Physiol       Date:  2010-10-06       Impact factor: 8.340

2.  Subunit F modulates ATP binding and migration in the nucleotide-binding subunit B of the A(1)A(O) ATP synthase of Methanosarcina mazei Gö1.

Authors:  Devanathan Raghunathan; Shovanlal Gayen; Anil Kumar; Cornelia Hunke; Gerhard Grüber; Chandra S Verma
Journal:  J Bioenerg Biomembr       Date:  2012-02-14       Impact factor: 2.945

3.  Protein dynamics investigated by inherent structure analysis.

Authors:  Francesco Rao; Martin Karplus
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-30       Impact factor: 11.205

4.  A hydrodynamic view of the first-passage folding of Trp-cage miniprotein.

Authors:  Vladimir A Andryushchenko; Sergei F Chekmarev
Journal:  Eur Biophys J       Date:  2015-11-12       Impact factor: 1.733

5.  Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations.

Authors:  Xiaoliang Pan; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2015-04-15       Impact factor: 2.991

6.  Alpha-Helix folding in the presence of structural constraints.

Authors:  Janne A Ihalainen; Beatrice Paoli; Stefanie Muff; Ellen H G Backus; Jens Bredenbeck; G Andrew Woolley; Amedeo Caflisch; Peter Hamm
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-09       Impact factor: 11.205

7.  Molecular simulations of a dynamic protein complex: role of salt-bridges and polar interactions in configurational transitions.

Authors:  Liqun Zhang; Matthias Buck
Journal:  Biophys J       Date:  2013-11-19       Impact factor: 4.033

8.  Structural requirements of the human sodium-dependent bile acid transporter (hASBT): role of 3- and 7-OH moieties on binding and translocation of bile acids.

Authors:  Pablo M González; Carlos F Lagos; Weslyn C Ward; James E Polli
Journal:  Mol Pharm       Date:  2013-12-26       Impact factor: 4.939

Review 9.  A gating mechanism of pentameric ligand-gated ion channels.

Authors:  Nicolas Calimet; Manuel Simoes; Jean-Pierre Changeux; Martin Karplus; Antoine Taly; Marco Cecchini
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-16       Impact factor: 11.205

10.  Binding of NAD+ and L-threonine induces stepwise structural and flexibility changes in Cupriavidus necator L-threonine dehydrogenase.

Authors:  Shogo Nakano; Seiji Okazaki; Hiroaki Tokiwa; Yasuhisa Asano
Journal:  J Biol Chem       Date:  2014-02-20       Impact factor: 5.157
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