open3spn2
An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM
Science Score: 49.0%
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✓DOI references
Found 6 DOI reference(s) in README -
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2 of 9 committers (22.2%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary
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Repository
An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM
Basic Info
- Host: GitHub
- Owner: cabb99
- License: mit
- Language: Python
- Default Branch: master
- Size: 32.9 MB
Statistics
- Stars: 18
- Watchers: 4
- Forks: 8
- Open Issues: 4
- Releases: 7
Topics
Metadata Files
README.md
Open-3SPN2
A Implementation of the 3SPN.2 and 3SPN.2C coarse-grained molecular model of DNA in OpenMM.
3SPN.2 and 3SPN.2C are DNA coarse-grained forcefields developed by the de Pablo group. Each DNA nucleotide is modelled by 3 beads: one bead for the phosphate, a second one for the sugar and a third one nucleobase. These forcefields were adapted by the Wolynes group to model protein-DNA interactions as a complement for the AWSEM coarse-grained protein forcefield.
Installation
Installation of the open3SPN2 repository is available through anaconda.
conda install -c conda-forge open3spn2
For protein-DNA simulations you will also need to install openAWSEM and add the openAWSEM path to the $PYTHONPATH environment variable. In linux you can set the path variables on ~/.bashrc.
export PYTHONPATH=/path/to/openAWSEM:$PYTHONPATH
Documentation
Further documentation and tutorials are hosted in readthedocs.
Acknowledgment
Carlos Bueno was supported by the MolSSI Software Fellowship, under the mentorship of Jessica Nash. We thank AMD (Advanced Micro Devices, Inc.) for the donation of high-performance computing hardware and HPC resources. This project is also supported by the Center for Theoretical Biological Physics (NSF Grants PHY-2019745 and PHY-1522550), with additional support from the D.R. Bullard Welch Chair at Rice University (Grant No. C-0016 to PGW).
Citations
If you publish any work using the open3SPN2 package, please include the following references:
Open3SPN2 Lu, W., Bueno, C., Schafer, N. P., Moller, J., Jin, S., Chen, X., ... & Wolynes, P. G. (2021). OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PLoS computational biology, 17(2), e1008308. https://doi.org/10.1371/journal.pcbi.1008308
3SPN.2C Freeman, G. S., Hinckley, D. M., Lequieu, J. P., Whitmer, J. K., & De Pablo, J. J. (2014). Coarse-grained modeling of DNA curvature. Journal of Chemical Physics, 141(16). https://doi.org/10.1063/1.4897649
3SPN.2 Hinckley, D. M., Freeman, G. S., Whitmer, J. K., & De Pablo, J. J. (2013). An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization. Journal of Chemical Physics, 139(14). https://doi.org/10.1063/1.4822042
Owner
- Name: Carlos Bueno
- Login: cabb99
- Kind: user
- Location: Houston, Texas
- Company: Rice University
- Repositories: 7
- Profile: https://github.com/cabb99
Research Assistant. Center for Theoretical Biophysics (CTBP)
GitHub Events
Total
- Issue comment event: 2
- Push event: 2
- Pull request review comment event: 1
- Pull request review event: 1
- Pull request event: 1
Last Year
- Issue comment event: 2
- Push event: 2
- Pull request review comment event: 1
- Pull request review event: 1
- Pull request event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| cabb99 | c****o@r****u | 144 |
| Carlos Bueno | c****9@g****m | 36 |
| luwei0917 | l****7@g****m | 10 |
| Cryosky | 5****5@q****m | 5 |
| Joshua Lequieu | l****u@m****u | 5 |
| Sourcery AI | 3 | |
| Riccardo Alessandri | r****i@g****m | 1 |
| groupdepablo | 3****o | 1 |
| Rebekah Wang | 9****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 10
- Total pull requests: 16
- Average time to close issues: 21 days
- Average time to close pull requests: 23 days
- Total issue authors: 7
- Total pull request authors: 5
- Average comments per issue: 2.4
- Average comments per pull request: 0.31
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 6
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 2.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- yihengwuKP (2)
- cabb99 (2)
- CryoSky (2)
- jmoller93 (1)
- MasatakaYm (1)
- Heezch (1)
- rmons01 (1)
Pull Request Authors
- cabb99 (6)
- sourcery-ai[bot] (5)
- stevenluo22 (3)
- ricalessandri (1)
- MengyanWang (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 49 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 7
- Total maintainers: 1
pypi.org: open3spn2
- Homepage: https://github.com/cabb99/open3spn2
- Documentation: https://open3spn2.readthedocs.io/
- License: MIT
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Latest release: 0.3.2
published over 2 years ago
Rankings
Maintainers (1)
Dependencies
- biopython *
- mdtraj *
- nose *
- numpy *
- openmm *
- pandas *
- pdbfixer *
- scipy *