Use Markdown.
https://www.alphafold.ebi.ac.uk/
https://github.com/deepmind/alphafold
https://github.com/sokrypton/ColabFold
A PyTorch reproduction of DeepMind's AlphaFold 2 and code to train the model.
https://github.com/aqlaboratory/openfold
Modified the open-source code of DeepMind AlphaFold v2.0 and code to train the model from scratch
https://github.com/deepmodeling/Uni-Fold
AF2Complex is an enhanced version of AlphaFold with many features useful for real-world application scenarios
https://github.com/FreshAirTonight/af2complex
Multi-state modeling of protein structures using AlphaFold based on custom template databases
https://github.com/huhlim/alphafold-multistate
Collection of scripts to survey a directory of alphafold multimer runs. It will go in each directory and make pLDDT and PAE plots delimited by sequence, provided the results directory contains a .fasta of the sequence. Will make all summary files and plot all PAE, pLDDT etc.
https://github.com/grandrea/Alphafold-analysis
Drawing PAE and MSA plots
https://git.embl.de/gchojnowski/af2plots
Run AlphaFold2 and ColabFold locally using common command line interface
https://git.embl.de/gchojnowski/af2wrapper
https://github.com/RosettaCommons/RoseTTAFold
https://github.com/Zuricho/ParallelFold
The old fork that includes command line version of the old ColabFold notebook. To be deprecated but still useful until ColabFold brings back the "old" sokrypton_alphafold2_advanced mode to batch.
https://github.com/jkosinski/alphafold/tree/sokrypton_alphafold2_advanced
Code for modeling multiple conformations with AlphaFold for this paper: https://www.biorxiv.org/content/10.1101/2021.11.22.469536v1
https://github.com/delalamo/af2_conformations
https://github.com/tristanic/pae_to_domains