How to predict structures with AlphaFold: Difference between revisions
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* New in 2022<ref name="colabfold">PMID: 35637307</ref>: [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb ColabFold AlphaFold2_advanced]. Predicts homo- and hetero-multimers using methods from the Steinegger/Mirdita team<ref name="colabfold" /><ref name="colabfold2024">PMID: 39402428</ref>, before AlphaFold-multimer<ref name="afmultimer">[https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1.full Protein complex prediction with AlphaFold-Multimer], Preprint, Evans et al. 2021.</ref> was available. Does NOT use templates. [https://www.ebi.ac.uk/training/online/courses/alphafold/accessing-and-predicting-protein-structures-with-alphafold/predicting-protein-structures-with-colabfold-and-alphafold-colab/ See Instructions from EMBL-EBI]. | * New in 2022<ref name="colabfold">PMID: 35637307</ref>: [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb ColabFold AlphaFold2_advanced]. Predicts homo- and hetero-multimers using methods from the Steinegger/Mirdita team<ref name="colabfold" /><ref name="colabfold2024">PMID: 39402428</ref>, before AlphaFold-multimer<ref name="afmultimer">[https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1.full Protein complex prediction with AlphaFold-Multimer], Preprint, Evans et al. 2021.</ref> was available. Does NOT use templates. [https://www.ebi.ac.uk/training/online/courses/alphafold/accessing-and-predicting-protein-structures-with-alphafold/predicting-protein-structures-with-colabfold-and-alphafold-colab/ See Instructions from EMBL-EBI]. | ||
*New in 2022<ref name="af2021">PMID: 34265844</ref> | *New in 2022<ref name="af2021">PMID: 34265844</ref><ref name="afmultimer" />: [https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb AlphaFold2/Multimer Colab] able to predict protein multimers. From the DeepMind team<ref name="af2021" /><ref name="afmultimer" />. | ||
*New in 2022<ref name="alphafill">PMID: 36424442</ref>: [https://alphafill.eu/ AlphaFill] “transplants” missing ligands, cofactors and (metal) ions into AlphaFold models. From the Perrakis team<ref name="alphafill" />. Ligand positioning is approximate. See [[Alphafold#Ligands:_AlphaFill |CAUTION]] provided by the AlphaFill team. | *New in 2022<ref name="alphafill">PMID: 36424442</ref>: [https://alphafill.eu/ AlphaFill] “transplants” missing ligands, cofactors and (metal) ions into AlphaFold models. From the Perrakis team<ref name="alphafill" />. Ligand positioning is approximate. See [[Alphafold#Ligands:_AlphaFill |CAUTION]] provided by the AlphaFill team. | ||
