feflow
Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
Science Score: 77.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
1 of 7 committers (14.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.5%) to scientific vocabulary
Keywords from Contributors
Repository
Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
Basic Info
- Host: GitHub
- Owner: OpenFreeEnergy
- License: mit
- Language: Python
- Default Branch: main
- Size: 250 KB
Statistics
- Stars: 14
- Watchers: 6
- Forks: 2
- Open Issues: 55
- Releases: 4
Metadata Files
README.md
FE Flow
Recipes, utilities, and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
Copyright
Copyright (c) 2023, ChoderaLab Copyright (c) 2024, The Open Free Energy development team
Acknowledgements
Project based on the Computational Molecular Science Python Cookiecutter version 1.1.
References
[1] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30.
[2] Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex Ivy Zhang, Dominic A. Rufa, Iván Pulido, Michael M. Henry, Laura E. Rosen, Kevin Hauser, Sukrit Singh, and John D. Chodera Journal of Chemical Theory and Computation 2023 19 (15), 4863-4882 DOI: 10.1021/acs.jctc.3c00333
[3] Chodera, J. et al., 2023. choderalab/openmmtools: 0.23.1.
[4] Eastman, P. et al., 2017. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics R. Gentleman, ed.. PLOS Computational Biology, 13(7), p.1005659.
Owner
- Name: Open Free Energy
- Login: OpenFreeEnergy
- Kind: organization
- Website: https://openfree.energy
- Repositories: 10
- Profile: https://github.com/OpenFreeEnergy
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: FEflow
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Iván
family-names: Pulido Sánchez
orcid: 'https://orcid.org/0000-0002-7178-8136'
- given-names: Irfan
family-names: Alibay
orcid: 'https://orcid.org/0000-0001-5787-9130'
- given-names: David
family-names: Dotson
orcid: 'https://orcid.org/0000-0001-5879-2942'
- given-names: Richard
family-names: Gowers
orcid: 'https://orcid.org/0000-0002-3241-1846'
- given-names: Hannah
family-names: Baumann
orcid: 'https://orcid.org/0000-0002-1736-7744'
- given-names: Michael M.
family-names: Henry
orcid: 'https://orcid.org/0000-0002-3870-9993'
repository-code: 'https://github.com/OpenFreeEnergy/feflow'
version: '0.1'
date-released: '2024-07-29'
GitHub Events
Total
- Create event: 15
- Release event: 3
- Issues event: 16
- Watch event: 2
- Delete event: 14
- Issue comment event: 50
- Push event: 56
- Pull request review comment event: 11
- Pull request review event: 23
- Pull request event: 31
- Fork event: 1
Last Year
- Create event: 15
- Release event: 3
- Issues event: 16
- Watch event: 2
- Delete event: 14
- Issue comment event: 50
- Push event: 56
- Pull request review comment event: 11
- Pull request review event: 23
- Pull request event: 31
- Fork event: 1
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Iván Pulido | 2****s | 49 |
| David Dotson | d****l@g****m | 14 |
| pre-commit-ci[bot] | 6****] | 5 |
| Mike Henry | 1****y | 4 |
| jthorton | J****n@n****k | 4 |
| Irfan Alibay | I****y | 3 |
| Ethan Holz | e****z@t****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 64
- Total pull requests: 67
- Average time to close issues: 3 months
- Average time to close pull requests: 28 days
- Total issue authors: 10
- Total pull request authors: 9
- Average comments per issue: 0.75
- Average comments per pull request: 1.72
- Merged pull requests: 48
- Bot issues: 0
- Bot pull requests: 7
Past Year
- Issues: 32
- Pull requests: 35
- Average time to close issues: 26 days
- Average time to close pull requests: 6 days
- Issue authors: 8
- Pull request authors: 7
- Average comments per issue: 0.72
- Average comments per pull request: 1.2
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 5
Top Authors
Issue Authors
- ijpulidos (24)
- IAlibay (11)
- jthorton (2)
- dotsdl (2)
- mikemhenry (2)
- atravitz (1)
- jameseastwood (1)
- sukritsingh (1)
Pull Request Authors
- ijpulidos (37)
- mikemhenry (10)
- pre-commit-ci[bot] (9)
- IAlibay (9)
- jthorton (4)
- dotsdl (4)
- richardjgowers (2)
- ethanholz (2)
- ianmkenney (1)