Literature DB >> 16917862

Software news and updates. Carma: a molecular dynamics analysis program.

Nicholas M Glykos1.   

Abstract

A computer program has been developed to aid the analysis of molecular dynamics trajectories. The program is tuned for macromolecular large-scale problems and supports features such as removal of global translations-rotations of the solute, calculation of average distance maps and their corresponding standard deviations, calculation of the variance-covariance and cross-correlation matrices, and principal component analysis of trajectories with the added ability to create artificial trajectories based on selected eigenvectors. Limited graphics (trajectory viewing) capabilities are also available. (c) 2006 Wiley Periodicals, Inc. J Comput Chem, 2006.

Mesh：

Substances：

Year:  2006        PMID： 16917862     DOI： 10.1002/jcc.20482

Source DB:  PubMed          Journal:  J Comput Chem        ISSN： 0192-8651            Impact factor:   3.376


  141 in total

1.  Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking.

Authors:  Pandian Sokkar; Shylajanaciyar Mohandass; Murugesan Ramachandran
Journal:  J Mol Model       Date:  2010-10-06       Impact factor: 1.810

2.  Three force fields' views of the 3(10) helix.

Authors:  Kalliopi K Patapati; Nicholas M Glykos
Journal:  Biophys J       Date:  2011-10-05       Impact factor: 4.033

3.  Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data.

Authors:  Athanasios S Baltzis; Nicholas M Glykos
Journal:  Protein Sci       Date:  2015-12-16       Impact factor: 6.725

4.  A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils.

Authors:  Nikolaos N Louros; Fotis A Baltoumas; Stavros J Hamodrakas; Vassiliki A Iconomidou
Journal:  J Comput Aided Mol Des       Date:  2016-01-11       Impact factor: 3.686

5.  Dynamics of Recognition between tRNA and elongation factor Tu.

Authors:  John Eargle; Alexis A Black; Anurag Sethi; Leonardo G Trabuco; Zaida Luthey-Schulten
Journal:  J Mol Biol       Date:  2008-02-04       Impact factor: 5.469

6.  Molecular-dynamics simulations of insertion of chemically modified DNA nanostructures into a water-chloroform interface.

Authors:  Jianping Lin; Nadrian C Seeman; Nagarajan Vaidehi
Journal:  Biophys J       Date:  2008-05-02       Impact factor: 4.033

7.  Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase.

Authors:  Lauren M Adams; Ryan J Andrews; Quin H Hu; Heidi L Schmit; Sanchita Hati; Sudeep Bhattacharyya
Journal:  Biophys J       Date:  2019-08-31       Impact factor: 4.033

8.  The C-terminal Helix of Pseudomonas aeruginosa Elongation Factor Ts Tunes EF-Tu Dynamics to Modulate Nucleotide Exchange.

Authors:  Evelina Ines De Laurentiis; Evan Mercier; Hans-Joachim Wieden
Journal:  J Biol Chem       Date:  2016-09-13       Impact factor: 5.157

9.  Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.

Authors:  Mathieu Fossépré; Laurence Leherte; Aatto Laaksonen; Daniel P Vercauteren
Journal:  J Mol Model       Date:  2016-08-26       Impact factor: 1.810

10.  Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase.

Authors:  Gema L Ramírez-Salinas; J García-Machorro; Miguel Quiliano; Mirko Zimic; Verónica Briz; Saul Rojas-Hernández; J Correa-Basurto
Journal:  J Mol Model       Date:  2015-10-26       Impact factor: 1.810
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.