Protein structure prediction tools on COSMIC2

COSMIC² is a platform that runs protein structure prediction jobs at the San Diego Supercomputer Center. Unlike Google Colab notebooks, COSMIC2 jobs run on high-performance computing GPU nodes and have a maximum run time of 48 hours.

We currently offer the following tools:

To learn more about the differences between these tools, check out this blog post.

Grouped by job type

  • Predict single protein structure
    • AlphaFold2
    • ColabFold
    • OmegaFold
  • Predict structure of protein complex (>1 protein sequence)
    • AlphaFold Multimer
    • ColabFold
  • Predict antibody structure
    • IgFold

But wait, what’s the difference between AlphaFold Multimer & ColabFold?

AlphaFold Multimer runs the bona fide AlphaFold Multimer code released by DeepMind. ColabFold is a modified AlphaFold Multimer, where the multiple sequence alignment step is replaced by interrogating a mmseq database.

Recommendation: Start with ColabFold first since it is faster and produces similar results to AlphaFold Multimer.  If you are not getting high quality predictions from ColabFold, then try AlphaFold Multimer.