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For users interested in running large volumes of predictions with LocalColabFold, we strongly recommend getting familiar with the local mmseqs2 alignment procedure (https://harvardmed.atlassian.net/wiki/spaces/O2/pages/2180546561/Using+Local+ColabFold+on+O2#Generating-MSAs-Using-Local-MMseqs2 ). This is crucial to avoid getting bottlenecked or blacklisted by the remote server.
A direct link to the AlphaFold database mentioned at the top of the flowchart below can be found here.
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Please contact rchelp@hms.harvard.edu for any questions or clarification.