How to predict structures with AlphaFold: Difference between revisions

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'''Colabs''': After multiple free jobs in a Colab, a new job may be refused. You may be informed that a GPU could not be assigned. In 2024, a subscription to [https://colab.research.google.com/signup/pricing Colab Pro] is US $10/month. Paying this will enable you to do many more jobs.
'''Colabs''': After multiple free jobs in a Colab, a new job may be refused. You may be informed that a GPU could not be assigned. In 2024, a subscription to [https://colab.research.google.com/signup/pricing Colab Pro] is US $10/month. Paying this will enable you to do many more jobs.
==Single chain limitation==
Initially, AlphaFold and ColabFold performed best with single chains<ref name="complexes">[https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1 Protein complex prediction with AlphaFold-Multimer], 2021, Evans ''et al.'' (DeepMind Team).</ref>, which may include one or a few domains. The instructions below were written before ColabFold was adapted to prediction of complexes or alternate conformations.
If you are interested in complexes or alternate conformations, please see ColabFold instructions in the 2023 paper by Kim ''et al.'' <ref name="kim2023">[https://protocolexchange.researchsquare.com/article/pex-2490/v1 Easy and accurate protein structure prediction using ColabFold], 2023, Kim ''et al.'' (DeepMind Team).</ref>


==Instructions for ColabFold==
==Instructions for ColabFold==
In 2024, ColabFold is not necessarily the best or only place to submit you job: see above. This procedure was written in 2022. Some of the options recommended below were gleaned from the [https://www.youtube.com/watch?v=Rfw7thgGTwI 1 hour 46 minute video of presentations by Sergey Ovchinnikov and Martin Steinegger] (August, 2021) for the Boston Protein Design and Modeling Club
In 2024, ColabFold is not necessarily the best or only place to submit you job: see above. This procedure was written in 2022. Some of the options recommended below were gleaned from the [https://www.youtube.com/watch?v=Rfw7thgGTwI 1 hour 46 minute video of presentations by Sergey Ovchinnikov and Martin Steinegger] (August, 2021) for the Boston Protein Design and Modeling Club
hosted by Chris Bahl.
hosted by Chris Bahl.
Initially, AlphaFold and ColabFold performed best with '''single chains'''<ref name="complexes">[https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1 Protein complex prediction with AlphaFold-Multimer], 2021, Evans ''et al.'' (DeepMind Team).</ref>, which may include one or a few domains. The instructions below were written '''before ColabFold was adapted to prediction of multimers'''. If you are interested in complexes or alternate conformations, please see ColabFold instructions in the 2023 paper by Kim ''et al.'' <ref name="kim2023">[https://protocolexchange.researchsquare.com/article/pex-2490/v1 Easy and accurate protein structure prediction using ColabFold], 2023, Kim ''et al.'' (DeepMind Team).</ref>


===Submitting A Sequence===
===Submitting A Sequence===
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