ColabDesign (EXPERIMENTAL justktln2 REMIX)

The only modification to the forked branch has been to introduce I/O with MDTraj and vectorize ProteinMPNN sampling across trajectories. In principle it is possible to do this with any conformational ensemble with a fixed protein topology, so this could be used with structures generated by AlphaFold MSA subsampling. You will therefore need to install MDTraj to use this. The important parts of this will be refactored and folded into either ciMIST or ColabDesign.

Original README, which I had nothing to do with, follows.

Making Protein Design accessible to all via Google Colab!

• P(structure | sequence)
  • TrDesign - using TrRosetta for design
  • AfDesign - using AlphaFold for design
  • [WIP] RfDesign - using RoseTTAFold for design
• P(sequence | structure)
  • ProteinMPNN
  • [WIP] TrMRF
• P(sequence)
  • [WIP] MSA_transformer
  • [WIP] SEQ - (GREMLIN, mfDCA, arDCA, plmDCA, bmDCA, etc)
• P(structure)
  • Rfdiffusion

Where can I chat with other ColabDesign users?

• See our Discord channel!

Presentations

Slides Talk

Contributors:

• Sergey Ovchinnikov @sokrypton
• Shihao Feng @JeffSHF
• Justas Dauparas @dauparas
• Weikun.Wu @guyujun (from Levinthal.bio)
• Christopher Frank @chris-kafka