Alphafold/Colabfold
About Alphafold/Colabfold
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
Info Sessions / Town Halls
Thank you to those who attended our Townhall on June 8th! The following resources from that event are below:
Townhall slides:
Dr. Sergey Ovchinnikov
• Introduction to AlphaFold & ColabFold and what they’re for, examples of input & output
• Slides for Dr. Ovchinnikov’s presentation
Slides for CCB/RC
• Running AlphaFold/ColabFold on O2 – Alex Truong, Calvin Cox, Roger Vargas
• Slides for CCB/RC Presentation
Dr. Mohammed AlQuraishi
• OpenFold: A trainable implementation of AlphaFold
• Colab
• Github page
Dr. Jason Key
• SBGrid & BioGrids: how to further evaluate predictions from AlphaFold/ColabFold
• Slide for Dr. Key’s Presentation