https://github.com/choderalab/yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.0%) to scientific vocabulary
Keywords
alchemical
alchemical-free-energy-calculations
drug-discovery
free-energy
free-energy-perturbation
molecular-dynamics
molecular-dynamics-simulation
mskcc
openmm
python
Keywords from Contributors
molecular-simulations
expanded-ensembles
molecular-design
relative-free-energy
free-energy-calculations
integrators
markov-chain-monte-carlo
mcmc
replica-exchange
computational-chemistry
Last synced: 6 months ago
·
JSON representation
Repository
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Basic Info
- Host: GitHub
- Owner: choderalab
- License: mit
- Language: Python
- Default Branch: master
- Homepage: http://getyank.org
- Size: 45.3 MB
Statistics
- Stars: 171
- Watchers: 24
- Forks: 69
- Open Issues: 243
- Releases: 47
Topics
alchemical
alchemical-free-energy-calculations
drug-discovery
free-energy
free-energy-perturbation
molecular-dynamics
molecular-dynamics-simulation
mskcc
openmm
python
Created over 12 years ago
· Last pushed over 2 years ago
Metadata Files
Readme
License
README.md
YANK
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations
Documentation
Documentation, tutorials, and best practices can be found at getyank.org.
Getting Started
See the Quickstart instructions.
Examples
Examples are available in the yank-examples repository:
bash
git clone https://github.com/choderalab/yank-examples.git
Maintainers
- Andrea Rizzi
<andrea.rizzi@choderalab.org>(WCMC) - Hannah Bruce Macdonald
<hannah.brucemacdonald>(MSKCC) - John D. Chodera
<john.chodera@choderalab.org>(MSKCC) - Levi N. Naden
<levi.naden@choderalab.org>(MSKCC)
Contributors
- Kim Branson (Stanford)
- Kyle A. Beauchamp (MSKCC)
- Peter M. Eastman (Stanford)
- Mark Friedrichs (Stanford)
- Imran Haque (Stanford)
- Patrick B. Grinaway (MSKCC)
- Christoph Klein (University of Virginia)
- Rosa Luirink (VU Amsterdam)
- Daniel L. Parton (MSKCC)
- Randy Radmer (Stanford)
- Arien Sebastian Rustenburg (MSKCC)
- Michael Shirts (University of Colorado Boulder)
- Kai Wang (University of Virginia)
Owner
- Name: Chodera lab // Memorial Sloan Kettering Cancer Center
- Login: choderalab
- Kind: organization
- Email: john.chodera@choderalab.org
- Location: Memorial Sloan-Kettering Cancer Center, Manhattan, NY
- Website: http://choderalab.org
- Repositories: 269
- Profile: https://github.com/choderalab
GitHub Events
Total
- Issues event: 4
- Watch event: 10
- Issue comment event: 3
- Fork event: 2
Last Year
- Issues event: 4
- Watch event: 10
- Issue comment event: 3
- Fork event: 2
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Andrea Rizzi | a****i@g****m | 937 |
| John Chodera (MSKCC) | c****j@m****g | 567 |
| Levi Naden | l****n@c****g | 549 |
| John Chodera | j****a@c****g | 202 |
| pgrinaway | w****o | 63 |
| kyleabeauchamp | k****p@g****m | 60 |
| Andrea Rizzi | a****i@c****g | 46 |
| steven-albanese | s****1@g****m | 17 |
| Chodera | c****j@m****g | 7 |
| Grinaway | g****p@l****g | 6 |
| Jaime Rodríguez-Guerra | j****p@u****m | 6 |
| Diego Prada | p****a@g****m | 6 |
| SimonBoothroyd | s****d@c****g | 4 |
| steven-albanese | a****s@l****g | 4 |
| Bas Rustenburg | b****g@c****g | 3 |
| Jeffrey Comer | j****r@g****m | 3 |
| Patrick Grinaway | p****y@g****m | 2 |
| Kevin Boehm | b****k@l****e | 2 |
| Mike Henry | 1****y@u****m | 2 |
| Hannah Bruce Macdonald | 4****d@u****m | 1 |
| Andrea Rizzi | a****i@h****t | 1 |
| Patrick Grinaway | p****y@d****g | 1 |
| Naden | n****l@l****l | 1 |
| Jaime RGP | j****e@g****m | 1 |
| Guowei Qi | g****i@r****m | 1 |
| Bas | b****g@u****m | 1 |
| Jürgen Gmach | j****h@g****m | 1 |
| Silveira | s****a@l****g | 1 |
| Shyam Saladi | s****i@u****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: over 2 years ago
All Time
- Total issues: 86
- Total pull requests: 16
- Average time to close issues: 9 months
- Average time to close pull requests: 7 months
- Total issue authors: 52
- Total pull request authors: 10
- Average comments per issue: 2.74
- Average comments per pull request: 2.38
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 16
- Pull requests: 1
- Average time to close issues: about 2 months
- Average time to close pull requests: 2 months
- Issue authors: 15
- Pull request authors: 1
- Average comments per issue: 1.31
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kingljy0818 (9)
- jchodera (5)
- isjoung (3)
- Byun-jinyoung (3)
- therealchrisneale (3)
- mmagithub (3)
- mjw99 (3)
- kadiliissaar (3)
- daveminh (2)
- Eli-VDB (2)
- mattwthompson (2)
- gsabbih6 (2)
- zhang-ivy (2)
- dxli75 (2)
- kexul (2)
Pull Request Authors
- mikemhenry (4)
- jfennick (2)
- jchodera (2)
- mattwthompson (2)
- evohringer (1)
- jaimergp (1)
- jeffcomer (1)
- ajsilveira (1)
- hannahbrucemacdonald (1)
- lilyminium (1)
Top Labels
Issue Labels
bug (5)
enhancement (3)
error handling (1)
refactoring (1)
testing (1)
Priority high (1)
repex (1)
critical (1)
question (1)
documentation (1)
examples (1)
Priority low (1)
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 2
- Total dependent repositories: 1
- Total versions: 1
conda-forge.org: yank
YANK is a testbed for experimenting with algorithms for the efficient computation of small molecule binding free energies to biomolecular targets using alchemical methods. YANK is built on OpenMM, the API for molecular simulation, and uses its GPU-accelerated library implementation for hardware acceleration.
- Homepage: http://getyank.org/
- License: MIT
-
Latest release: 0.25.2
published about 5 years ago
Rankings
Dependent packages count: 19.6%
Forks count: 22.0%
Average: 23.7%
Dependent repos count: 24.2%
Stargazers count: 29.2%
Last synced:
7 months ago
Dependencies
docs/requirements.txt
pypi
- jinja2 *
- runipy *
- sphinx *
- sphinx_rtd_theme *
.github/workflows/CI.yaml
actions
- actions/checkout v2 composite
- codecov/codecov-action v1 composite
- conda-incubator/setup-miniconda v2 composite
Dockerfile
docker
- nvidia/cuda latest build
setup.py
pypi