Attendees

Tom Goddard, Zach, Greg, Elaine, Tom Ferrin

August 14, 2025

Agenda

• TomG, Boltz ligand affinity, Animation examples. Slides

Discussion Notes

• Boltz structure prediction in ChimeraX
  • Demonstrated how to predict HIV protease dimer bound with a set of 50 ligands.
  • Not yet in daily build.
  • Benchmarks by others show ML ligand docking prediction is good for ligands and pockets that are similar to ones in training data (80% success), much worse if novel (20% success).
  • Future Boltz plans include new features (templates, pocket specification, post-translational modifications...) and memory optimization to predict larger structures.

• Animation examples
  • Showed example animations from Nature and Science papers.
  • Reviewed a list of problems in the example animations and tips to avoid them.

• ChimeraX help chatbot
  • Matthias Vorlander tried creating a ChimeraX help chatbot with Google NotebookLM.
  • Elaine reports that it worked quite well for 5 questions she tried.
  • Tried it during meeting.
  • TomG will reply to Matthias that we are interested in pursuing this.

Action Items