Attendees

Andrii Kyrylcuk, Zach, Eric, Tom Goddard, Greg, Elaine, Scooter, Tom Ferrin

December 4, 2025

Agenda

• Andrii Kyrylchuk, ViewDock demo and drug discovery projects
• Lab holiday card
• What to do with unused Cytoscape GPU nodes

Discussion Notes

• Holiday card
  • We will try Claude AI produced flotillin image for holiday card.
  • Tom Goddard and Elaine will work on it.

• Setup of GPU nodes
  • Tom G wants to use one of our 4 Nvidia L40S GPU nodes for Biophysics class for structure predictions.
  • Setting up node would require buying a 10 Gbit switch and copper to fiber adapter.
  • Node would be on a private network only visible from plato.
  • This will be hard for Biophysics students to access. Would require students have plato accounts (e.g. for ssh) or using an ssh tunnel from plato to the GPU node directly from their laptops with a password.
  • Too little time to set up hardware and software for early January class.

• ViewDock demo
  • Andrii discussed drug discovery pipeline.
  • Zinc database of about 10 billion compounds used for screening, cost about $10,000 per screen in computer time to run Dock.
  • Demonstrated ViewDock in ChimeraX.
  • Discussed "synton" fragment assembly docking to allow searching chemical space of trillions of compounds made by 3 reactions to attach 3 R groups from one of 30 million moieties.

• 3D glasses free displays
  • Andrii, Tom Goddard and Eric looked at ViewDock on Asus 3D glasses free display after group meeting.

Action Items