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StreaMD: Advanced analysis of molecular dynamics using R.

Dombrowsky, Maximilian J. and Jager, Sven and Schiller, Benjamin and Mayer, Benjamin E. and Stammler, Sebastian and Hamacher, Kay (2018):
StreaMD: Advanced analysis of molecular dynamics using R.
In: Journal of computational chemistry, 39 (21), pp. 1666-1674. ISSN 1096-987X,
[Article]

Abstract

Gromacs is one of the most popular molecular simulation suites currently available. In this contribution we present streaMD, the first interface between Gromacs trajectory files and the statistical language R. The amount of data created due to ever increasing computational power renders fast and efficient analysis of trajectories into a challenge. Especially as standard approaches such as root-mean square fluctuations and the like provide only limited physical insight. In our streaMD package integration of the Gromacs I/O libraries with advanced, graph-based analysis methods as the java library Stream leads to both: improved speed and analysis depth. We benchmark our results and highlight the applicability of the package by an interesting problem in RNA design, namely the interaction of tetracycline with an aptamer. © 2018 Wiley Periodicals, Inc.

Item Type: Article
Erschienen: 2018
Creators: Dombrowsky, Maximilian J. and Jager, Sven and Schiller, Benjamin and Mayer, Benjamin E. and Stammler, Sebastian and Hamacher, Kay
Title: StreaMD: Advanced analysis of molecular dynamics using R.
Language: English
Abstract:

Gromacs is one of the most popular molecular simulation suites currently available. In this contribution we present streaMD, the first interface between Gromacs trajectory files and the statistical language R. The amount of data created due to ever increasing computational power renders fast and efficient analysis of trajectories into a challenge. Especially as standard approaches such as root-mean square fluctuations and the like provide only limited physical insight. In our streaMD package integration of the Gromacs I/O libraries with advanced, graph-based analysis methods as the java library Stream leads to both: improved speed and analysis depth. We benchmark our results and highlight the applicability of the package by an interesting problem in RNA design, namely the interaction of tetracycline with an aptamer. © 2018 Wiley Periodicals, Inc.

Journal or Publication Title: Journal of computational chemistry
Journal volume: 39
Number: 21
Divisions: 10 Department of Biology
10 Department of Biology > Computational Biology and Simulation
Date Deposited: 24 Apr 2018 07:58
Identification Number: pmid:29665022
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