cgHeliParm
cgHeliParm is a python program that performs conformational analysis on coarse-grained Martini-based double-strand DNA molecules. It provides helical parameters such as base, base pair, and base pair step parameters. It can be used to analyze coarse-grain Martini molecular dynamics trajectories without transforming them into atomistic models.
Topic
Simulation experiment;Computational chemistry;DNA;Nucleic acid structure analysis
Detail
Operation: Molecular dynamics
Software interface: Command-line user interface
Language: Python
License: -
Cost: Free
Version name: -
Credit: The Netherlands Scientific Organization (NWO ChemThem program)
Input: -
Output: -
Contact: Ignacio Faustino i.faustino@rug.nl
Collection: -
Maturity: -
Publications
- cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations
- Faustino I, Marrink SJ. cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. Bioinformatics. 2017 Dec 1;33(23):3813-3815. doi: 10.1093/bioinformatics/btx444. PMID: 29036584.
- https://doi.org/10.1093/bioinformatics/btx444
- PMID: 29036584
- PMC: -
- 3DNA: a software package for the analysis, rebuilding and visualization of three‐dimensional nucleic acid structures
- Lu XJ, Olson WK. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 2003 Sep 1;31(17):5108-21. doi: 10.1093/nar/gkg680. PMID: 12930962; PMCID: PMC212791.
- https://doi.org/https://doi.org/10.1093/nar/gkg680
- PMID: 12930962
- PMC: PMC212791
Download and documentation
Documentation: http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/tutorial-martini-dna-gmx5#parameters
Home page: https://github.com/ifaust83/cgheliparm
Data: https://github.com/ifaust83/cgheliparm/tree/master/data
Links: https://github.com/ifaust83/cgheliparm/tree/master/examples
< Back to DB search