Protein Structure Prediction on O2

Research Computing now supports the use of several cutting-edge protein structure prediction options:

• Alphafold

• LocalColabFold

• OpenFold

For more details about the individual software, please refer to their respective documentation pages above.

As it may be difficult to determine which is the correct choice of program to leverage, we offer the following usage/troubleshooting flowchart helpfully generated by collaborators at the Center for Computational Medicine (CCB).

For users interested in running large volumes of predictions with LocalColabFold, we strongly recommend getting familiar with the local mmseqs2 alignment procedure (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.

Open

Please contact rchelp@hms.harvard.edu for any questions or clarification.