base on Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2  _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](https://github.com/deepmind/alphafold). # Documentation See our new home for docs at [openfold.readthedocs.io](https://openfold.readthedocs.io/en/latest/), with instructions for installation and model inference/training. Much of the content from this page may be found [here.](https://github.com/aqlaboratory/openfold/blob/main/docs/source/original_readme.md) ## 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](https://www.nature.com/articles/s41586-021-03819-2) and [AlphaFold-Multimer](https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1) if applicable. ", Assign "at most 3 tags" to the expected json: {"id":"10174","tags":[]} "only from the tags list I provide: [{"id":77,"name":"3d"},{"id":89,"name":"agent"},{"id":17,"name":"ai"},{"id":54,"name":"algorithm"},{"id":24,"name":"api"},{"id":44,"name":"authentication"},{"id":3,"name":"aws"},{"id":27,"name":"backend"},{"id":60,"name":"benchmark"},{"id":72,"name":"best-practices"},{"id":39,"name":"bitcoin"},{"id":37,"name":"blockchain"},{"id":1,"name":"blog"},{"id":45,"name":"bundler"},{"id":58,"name":"cache"},{"id":21,"name":"chat"},{"id":49,"name":"cicd"},{"id":4,"name":"cli"},{"id":64,"name":"cloud-native"},{"id":48,"name":"cms"},{"id":61,"name":"compiler"},{"id":68,"name":"containerization"},{"id":92,"name":"crm"},{"id":34,"name":"data"},{"id":47,"name":"database"},{"id":8,"name":"declarative-gui "},{"id":9,"name":"deploy-tool"},{"id":53,"name":"desktop-app"},{"id":6,"name":"dev-exp-lib"},{"id":59,"name":"dev-tool"},{"id":13,"name":"ecommerce"},{"id":26,"name":"editor"},{"id":66,"name":"emulator"},{"id":62,"name":"filesystem"},{"id":80,"name":"finance"},{"id":15,"name":"firmware"},{"id":73,"name":"for-fun"},{"id":2,"name":"framework"},{"id":11,"name":"frontend"},{"id":22,"name":"game"},{"id":81,"name":"game-engine "},{"id":23,"name":"graphql"},{"id":84,"name":"gui"},{"id":91,"name":"http"},{"id":5,"name":"http-client"},{"id":51,"name":"iac"},{"id":30,"name":"ide"},{"id":78,"name":"iot"},{"id":40,"name":"json"},{"id":83,"name":"julian"},{"id":38,"name":"k8s"},{"id":31,"name":"language"},{"id":10,"name":"learning-resource"},{"id":33,"name":"lib"},{"id":41,"name":"linter"},{"id":28,"name":"lms"},{"id":16,"name":"logging"},{"id":76,"name":"low-code"},{"id":90,"name":"message-queue"},{"id":42,"name":"mobile-app"},{"id":18,"name":"monitoring"},{"id":36,"name":"networking"},{"id":7,"name":"node-version"},{"id":55,"name":"nosql"},{"id":57,"name":"observability"},{"id":46,"name":"orm"},{"id":52,"name":"os"},{"id":14,"name":"parser"},{"id":74,"name":"react"},{"id":82,"name":"real-time"},{"id":56,"name":"robot"},{"id":65,"name":"runtime"},{"id":32,"name":"sdk"},{"id":71,"name":"search"},{"id":63,"name":"secrets"},{"id":25,"name":"security"},{"id":85,"name":"server"},{"id":86,"name":"serverless"},{"id":70,"name":"storage"},{"id":75,"name":"system-design"},{"id":79,"name":"terminal"},{"id":29,"name":"testing"},{"id":12,"name":"ui"},{"id":50,"name":"ux"},{"id":88,"name":"video"},{"id":20,"name":"web-app"},{"id":35,"name":"web-server"},{"id":43,"name":"webassembly"},{"id":69,"name":"workflow"},{"id":87,"name":"yaml"}]" returns me the "expected json"