openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

https://github.com/aqlaboratory/openfold

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: biorxiv.org, nature.com
✓
Committers with academic emails
5 of 48 committers (10.4%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (10.3%) to scientific vocabulary

Keywords

alphafold2 protein-structure pytorch

Keywords from Contributors

optimizing-compiler cryptocurrencies tensors embedded agents application multi-agents genomics datacleaner pipeline-testing

Last synced: 6 months ago · JSON representation ·

Repository

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Basic Info

Host: GitHub
Owner: aqlaboratory
License: apache-2.0
Language: Python
Default Branch: main
Homepage:
Size: 19 MB

Statistics

Stars: 3,096
Watchers: 46
Forks: 620
Open Issues: 223
Releases: 0

Topics

alphafold2 protein-structure pytorch

Created over 4 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation

README.md

header Figure: Comparison of OpenFold and AlphaFold2 predictions to the experimental structure of PDB 7KDX, chain B.

OpenFold

A faithful but trainable PyTorch reproduction of DeepMind's AlphaFold 2.

Documentation

See our new home for docs at openfold.readthedocs.io, with instructions for installation and model inference/training.

Much of the content from this page may be found here.

Copyright Notice

While AlphaFold's and, by extension, OpenFold's source code is licensed under the permissive Apache Licence, Version 2.0, DeepMind's pretrained parameters fall under the CC BY 4.0 license, a copy of which is downloaded to openfold/resources/params by the installation script. Note that the latter replaces the original, more restrictive CC BY-NC 4.0 license as of January 2022.

Contributing

If you encounter problems using OpenFold, feel free to create an issue! We also welcome pull requests from the community.

Citing this Work

Please cite our paper:

bibtex @article {Ahdritz2022.11.20.517210, author = {Ahdritz, Gustaf and Bouatta, Nazim and Floristean, Christina and Kadyan, Sachin and Xia, Qinghui and Gerecke, William and O{\textquoteright}Donnell, Timothy J and Berenberg, Daniel and Fisk, Ian and Zanichelli, Niccolò and Zhang, Bo and Nowaczynski, Arkadiusz and Wang, Bei and Stepniewska-Dziubinska, Marta M and Zhang, Shang and Ojewole, Adegoke and Guney, Murat Efe and Biderman, Stella and Watkins, Andrew M and Ra, Stephen and Lorenzo, Pablo Ribalta and Nivon, Lucas and Weitzner, Brian and Ban, Yih-En Andrew and Sorger, Peter K and Mostaque, Emad and Zhang, Zhao and Bonneau, Richard and AlQuraishi, Mohammed}, title = {{O}pen{F}old: {R}etraining {A}lpha{F}old2 yields new insights into its learning mechanisms and capacity for generalization}, elocation-id = {2022.11.20.517210}, year = {2022}, doi = {10.1101/2022.11.20.517210}, publisher = {Cold Spring Harbor Laboratory}, URL = {https://www.biorxiv.org/content/10.1101/2022.11.20.517210}, eprint = {https://www.biorxiv.org/content/early/2022/11/22/2022.11.20.517210.full.pdf}, journal = {bioRxiv} } If you use OpenProteinSet, please also cite:

bibtex @misc{ahdritz2023openproteinset, title={{O}pen{P}rotein{S}et: {T}raining data for structural biology at scale}, author={Gustaf Ahdritz and Nazim Bouatta and Sachin Kadyan and Lukas Jarosch and Daniel Berenberg and Ian Fisk and Andrew M. Watkins and Stephen Ra and Richard Bonneau and Mohammed AlQuraishi}, year={2023}, eprint={2308.05326}, archivePrefix={arXiv}, primaryClass={q-bio.BM} } Any work that cites OpenFold should also cite AlphaFold and AlphaFold-Multimer if applicable.

Owner

Name: AQ Laboratory
Login: aqlaboratory
Kind: organization
Email: m.alquraishi@columbia.edu
Location: Columbia University

Website: aqlab.io
Twitter: MoAlQuraishi
Repositories: 17
Profile: https://github.com/aqlaboratory

Citation (CITATION.cff)

cff-version: 1.2.0
preferred-citation:
    authors:
    - family-names: "Ahdritz"
      given-names: "Gustaf"
      orcid: https://orcid.org/0000-0001-8283-5324
    - family-names: "Bouatta"
      given-names: "Nazim"
      orcid: https://orcid.org/0000-0002-6524-874X
    - family-names: "Kadyan"
      given-names: "Sachin"
      orcid: https://orcid.org/0000-0002-6079-7627
    - family-names: "Xia"
      given-names: "Qinghui"
    - family-names: "Gerecke"
      given-names: "William"
      orcid: https://orcid.org/0000-0002-9777-6192
    - family-names: "O'Donnell"
      given-names: "Timothy J"
      orcid: https://orcid.org/0000-0002-9949-069X
    - family-names: "Berenberg"
      given-names: "Daniel"
      orcid: https://orcid.org/0000-0003-4631-0947
    - family-names: "Fisk"
      given-names: "Ian"
    - family-names: "Zanichelli"
      given-names: "Niccolò"
      orcid: https://orcid.org/0000-0002-3093-3587
    - family-names: "Zhang"
      given-names: "Bo"
      orcid: https://orcid.org/0000-0002-9714-2827
    - family-names: "Nowaczynski"
      given-names: "Arkadiusz"
      orcid: https://orcid.org/0000-0002-3351-9584
    - family-names: "Wang"
      given-names: "Bei"
      orcid: https://orcid.org/0000-0003-4942-9652
    - family-names: "Stepniewska-Dziubinska"
      given-names: "Marta M"
      orcid: https://orcid.org/0000-0003-4942-9652
    - family-names: "Zhang"
      given-names: "Shang"
      orcid: https://orcid.org/0000-0003-0759-2080
    - family-names: "Ojewole"
      given-names: "Adegoke"
      orcid: https://orcid.org/0000-0003-2661-4388
    - family-names: "Guney"
      given-names: "Murat Efe"
    - family-names: "Biderman"
      given-names: "Stella"
      orcid: https://orcid.org/0000-0001-8228-1042
    - family-names: "Watkins"
      given-names: "Andrew M"
      orcid: https://orcid.org/0000-0003-1617-1720
    - family-names: "Ra"
      given-names: "Stephen"
      orcid: https://orcid.org/0000-0002-2820-0050
    - family-names: "Lorenzo"
      given-names: "Pablo Ribalta"
      orcid: https://orcid.org/0000-0002-3657-8053
    - family-names: "Nivon"
      given-names: "Lucas"
    - family-names: "Weitzner"
      given-names: "Brian"
      orcid: https://orcid.org/0000-0002-1909-0961
    - family-names: "Ban"
      given-names: "Yih-En"
      orcid: https://orcid.org/0000-0003-3698-3574
    - family-names: "Ban"
      given-names: "Yih-En Andrew"
      orcid: https://orcid.org/0000-0003-3698-3574
    - family-names: "Sorger"
      given-names: "Peter K"
      orcid: https://orcid.org/0000-0002-3364-1838
    - family-names: "Mostaque"
      given-names: "Emad"
    - family-names: "Zhang"
      given-names: "Zhao"
      orcid: https://orcid.org/0000-0001-5921-0035
    - family-names: "Bonneau"
      given-names: "Richard"
      orcid: https://orcid.org/0000-0003-4354-7906
    - family-names: "AlQuraishi"
      given-names: "Mohammed"
      orcid: https://orcid.org/0000-0001-6817-1322
    title: "OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization"
    type: article
    doi: 10.1101/2022.11.20.517210
doi: 10.1101/2022.11.20.517210
date-released: 2021-11-12
url: "https://doi.org/10.1101/2022.11.20.517210"

GitHub Events

Total

Create event: 4
Release event: 1
Issues event: 43
Watch event: 319
Delete event: 1
Issue comment event: 80
Push event: 10
Pull request review event: 4
Pull request review comment event: 4
Pull request event: 33
Fork event: 93

Last Year

Create event: 4
Release event: 1
Issues event: 43
Watch event: 319
Delete event: 1
Issue comment event: 80
Push event: 10
Pull request review event: 4
Pull request review comment event: 4
Pull request event: 33
Fork event: 93

Committers

Last synced: 9 months ago

All Time

Total Commits: 1,410
Total Committers: 48
Avg Commits per committer: 29.375
Development Distribution Score (DDS): 0.562

Past Year

Commits: 33
Committers: 7
Avg Commits per committer: 4.714
Development Distribution Score (DDS): 0.485

Top Committers

Name	Email	Commits
Gustaf Ahdritz	g**z@g**m	617
jnwei	j**i@o**o	222
Geoffrey Yu	g**6@i**m	181
Sachin Kadyan	s**7@g**m	111
Christina Floristean	c**n@g**m	73
Dingquan Yu	g**u@G**l	20
Sam DeLuca	s**m@c**m	18
Jose Duarte	j**e@g**m	17
Lukas Jarosch	l**h@g**t	17
Vaclav Hanzl	6****l	16
Marta	m**s@n**m	13
Brian Loyal	b**l@a**m	10
Tim O'Donnell	t**l@g**m	9
etowahadams	e**s@g**m	8
rostro36	j**t@u**h	8
Matthew W. Thompson	m**n@p**m	6
Christian Clauss	c**s@m**m	6
Lucas Bickmann	l**3@u**e	6
dependabot[bot]	4****]	4
Nikita Smetanin	n**l@g**m	4
Kolja Stahl	k**l@t**e	4
Zhang690683220	z**a@l**n	3
Niccolò Zanichelli	6****9	3
Karl Leswing	k**g@g**m	3
Jonathan King	j**g@b**u	3
yoel shoshan	y**s@i**m	2
controny	0**i@g**m	2
awaelchli	a**i@g**m	2
Santi Villalba	s**l@g**m	2
Mohammed AlQuraishi	a****i	2
and 18 more...

Committer Domains (Top 20 + Academic)

nvidia.com: 2 omsf.io: 1 cyrusbio.com: 1 gmx.net: 1 amazon.com: 1 unibe.ch: 1 me.com: 1 uni-muenster.de: 1 tu-berlin.de: 1 live.cn: 1 berkeley.edu: 1 il.ibm.com: 1 computelab-frontend-2.nvidia.com: 1 computelab-frontend-3.nvidia.com: 1 fb.com: 1 sonic-ssh.entos-foundry.ai: 1 163.com: 1 mavs.uta.edu: 1 ryankosai.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 216
Total pull requests: 128
Average time to close issues: 29 days
Average time to close pull requests: 20 days
Total issue authors: 169
Total pull request authors: 49
Average comments per issue: 2.77
Average comments per pull request: 0.51
Merged pull requests: 75
Bot issues: 0
Bot pull requests: 3

Past Year

Issues: 38
Pull requests: 32
Average time to close issues: 7 days
Average time to close pull requests: 13 days
Issue authors: 31
Pull request authors: 15
Average comments per issue: 0.68
Average comments per pull request: 0.22
Merged pull requests: 12
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

abhinavb22 (6)
vaclavhanzl (5)
jong3 (4)
RJ3 (3)
agustin-ormazabal (3)
jonathanking (3)
liweiqing1997 (3)
brucejwittmann (3)
vetmax7 (3)
yuzimu1 (3)
Ottovonxu (2)
roivant-matts (2)
emzodls (2)
lucajovine (2)
tsjain (2)

Pull Request Authors

jnwei (27)
dingquanyu (17)
vaclavhanzl (14)
etowahadams (9)
ljarosch (8)
jnooree (4)
juliocesar-io (4)
josemduarte (4)
YoelShoshan (4)
amorehead (3)
jonathanking (3)
Lix1993 (3)
christinaflo (3)
an1lam (3)
dependabot[bot] (3)

Top Labels

Issue Labels

documentation (1)

Pull Request Labels

dependencies (3)

Packages

Total packages: 3
Total downloads:
- pypi 365 last-month

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 7
Total maintainers: 2

proxy.golang.org: github.com/aqlaboratory/openfold

Documentation: https://pkg.go.dev/github.com/aqlaboratory/openfold#section-documentation
License: apache-2.0
Latest release: v2.2.0+incompatible
published 10 months ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 6.5%

Average: 6.7%

Dependent repos count: 7.0%

Last synced: 6 months ago

pypi.org: openfold

A PyTorch reimplementation of DeepMind's AlphaFold 2

Homepage: https://github.com/aqlaboratory/openfold
Documentation: https://openfold.readthedocs.io/
License: Apache License, Version 2.0
Latest release: 0.0.1
published almost 3 years ago

Versions: 1
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 361 Last month
Docker Downloads: 0

Rankings

Stargazers count: 1.5%

Forks count: 2.8%

Dependent packages count: 7.4%

Average: 10.4%

Downloads: 18.0%

Dependent repos count: 22.2%

Maintainers (1)

juncongmoo

Last synced: 6 months ago

pypi.org: openfold2

A PyTorch reimplementation of DeepMind's AlphaFold 2

Homepage: https://github.com/aqlaboratory/openfold
Documentation: https://openfold2.readthedocs.io/
License: Apache License, Version 2.0
Latest release: 0.0.1
published almost 3 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 4 Last month

Rankings

Stargazers count: 1.6%

Forks count: 2.9%

Dependent packages count: 6.6%

Average: 15.2%

Dependent repos count: 30.6%

Downloads: 34.3%

Maintainers (1)

wufuheng

Last synced: 6 months ago

Dependencies

.github/workflows/docker-image.yml actions

actions/checkout v2 composite

.github/workflows/undefined_names.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

Dockerfile docker

nvidia/cuda 11.3.1-cudnn8-runtime-ubuntu18.04 build

environment.yml pypi

PyYAML ==5.4.1
biopython ==1.79
deepspeed ==0.5.10
dm-tree ==0.1.6
ml-collections ==0.1.0
modelcif ==0.7
numpy ==1.21.2
pytorch_lightning ==1.5.10
requests ==2.26.0
scipy ==1.7.1
tqdm ==4.62.2
typing-extensions ==3.10.0.2
wandb ==0.12.21

notebooks/environment.yml pypi

PyYAML ==5.4.1
biopython ==1.79
dm-tree ==0.1.6
ml-collections ==0.1.0
requests ==2.26.0
typing-extensions ==3.10.0.2

setup.py pypi