Dombrowsky, Maximilian J. ; Jager, Sven ; Schiller, Benjamin ; Mayer, Benjamin E. ; Stammler, Sebastian ; Hamacher, Kay (2018)
StreaMD: Advanced analysis of molecular dynamics using R.
In: Journal of computational chemistry, 39 (21)
Artikel, Bibliographie
Kurzbeschreibung (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.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2018 |
| Autor(en): | Dombrowsky, Maximilian J. ; Jager, Sven ; Schiller, Benjamin ; Mayer, Benjamin E. ; Stammler, Sebastian ; Hamacher, Kay |
| Art des Eintrags: | Bibliographie |
| Titel: | StreaMD: Advanced analysis of molecular dynamics using R. |
| Sprache: | Englisch |
| Publikationsjahr: | 5 August 2018 |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | Journal of computational chemistry |
| Jahrgang/Volume einer Zeitschrift: | 39 |
| (Heft-)Nummer: | 21 |
| Kurzbeschreibung (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. |
| ID-Nummer: | pmid:29665022 |
| Fachbereich(e)/-gebiet(e): | 10 Fachbereich Biologie 10 Fachbereich Biologie > Computational Biology and Simulation |
| Hinterlegungsdatum: | 24 Apr 2018 07:58 |
| Letzte Änderung: | 28 Aug 2018 06:36 |
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