AlphaFold: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Angel Herraez, Joel L. Sussman, Wayne Decatur

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 ==Free AlphaFold-based Servers==
-[http://github.com/sokrypton/ColabFold#making-protein-folding-accessible-to-all-via-google-colab A Guide to the free RoseTTAFold and AlphaFold 2 Colab notebooks]
-A [http://www.youtube.com/watch?v=Rfw7thgGTwI video covering an overview, comparison of some of the methods and how people are already extending them, how to submit and interpret, and a tutorial on how to use AlphaFold2 Colab] is available. The video was recorded on August 4th, 2021 presented by Sergey Ovchinnikov and Martin Steinegger, hosted by Chris Bahl for the Boston Protein Design and Modeling Club
 ===RoseTTAFold===
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 DeepMind has provided an [http://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb Alphafold Colab] that uses a "slightly simplified" version of AlphaFold version 2.0: "While accuracy will be near-identical to the full AlphaFold system on many targets, a small fraction have a large drop in accuracy due to the smaller MSA and lack of templates.". The AlphaFold Colab is '''free to use'''. The code is executed in a virtual machine private to your account, and data are stored on Google Drive. Nothing is installed on your computer; "everything happens in the cloud on Google Colab"<ref name="alphafoldcolab">[http://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb Alphafold Colab].</ref>
-For those unfamiliar with Colabs, the user interface may look unfamilar, but the instructions are clear and straightforward to use. The mentions of "Runtime -> Run after" refer to the Runtime pull-down menu at the very top of the page. Getting a result may take several hours.
+For those unfamiliar with Colabs, the user interface may look unfamiliar, but the instructions are clear and straightforward to use. The mentions of "Runtime -> Run after" refer to the Runtime pull-down menu at the very top of the page. Getting a result may take several hours.
+===Current offerings via Colab===
+Work is ongoing and other offerings have on Colab are now available, for RoseTTAFold and AlphaFold 2 Colab beside the ones detailed above. This summary guide & video should help in choosing how to analyze your proteins of interest:
+- [http://github.com/sokrypton/ColabFold#making-protein-folding-accessible-to-all-via-google-colab A Guide to the free RoseTTAFold and AlphaFold 2 Colab notebooks]
+- A [http://www.youtube.com/watch?v=Rfw7thgGTwI video covering an overview, comparison of some of the methods and how people are already extending them, how to submit and interpret, and a tutorial on how to use AlphaFold2 Colab] is available. The video was recorded on August 4th, 2021 presented by Sergey Ovchinnikov and Martin Steinegger, hosted by Chris Bahl for the Boston Protein Design and Modeling Club
 ==References==