AlphaFold & ColabFold

Work Group

Genetics / Genomics

Project Lead

Roger Vargas, PhD

Project Status

Ongoing

Project Deliverable

Protein Structure Prediction.

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.

Questions?

Contact Sunil Poudel with questions about this project.