2021-08-05 Meeting notes

LiveCoMS review

Chapin Cavender

• Emails sent to existing and new contributors inviting them to:

  • Edit outline to include key references and specific datasets

  • Volunteer to contribute text

• Update on responses

Dipeptide 2-D TorsionDrive

Chapin Cavender

• Pilot dataset to test feasibility of 2-D TorsionDrives for dipeptides

• Generated all rotamers of 27 dipeptides (Ace-X-Nme)

• 2-D TorsionDrive to scan phi and psi for:

  • Alanine dipeptide

  • Two rotamers of tryptophan dipeptide

Future QC datasets

Chapin Cavender

• Compare 2-D TorsionDrive to grid optimization (grid search with fast method followed by constrained optimization with accurate method)

• What should we include in the training dataset? We want to construct a hierarchy of high priority (small) to low priority (large) datasets.

  • How many side chains in QC molecules?

  • Which dihedrals to scan?

  • How many rotamers per side chain?

  • For tetrapeptides Ace-X-Y-Z-Nme

    • Which side chains should be included as central residues (Y)?

    • Which side chains should be included as flanking residues (X and Z)?