AlphaFold & ColabFold

Work Group

Project Lead(s)

Project Status

Complete

Project Deliverable

Modules on the O2 HPC cluster

Collaborator Name

Research Computing and Edward Huttlin, PHD

HMS Department

Cell Biology

Project Description

Alphafold (from DeepMind) & ColabFold are new tools for predicting protein structures. They are available as experimental modules on O2. This means that some features may not work as expected, as the code itself was not designed with standard HPC environments in mind. AlphaFold takes fewer parameters, and uses jackhmmer as an MSA generator instead of mmseqs2, which can make it slower than ColabFold for certain inputs. It may also require more resources to run so we recommend using ColabFold for protein structure prediction. CCB works on developing a pair of modules on the O2 HPC cluster to facilitate protein structure prediction.