2021-10-21 Meeting notes

LiveCoMS review

Chapin Cavender

External contributors are drafting text for sections on observables and on specific datasets

• RT crystal sections were submitted last Friday (2021-10-15)

• Solution NMR sections are expected this coming Friday (2021-10-22)

• OpenFF PIs please block off some time in the next week or two to provide comments/edits on this draft

TODOs

• Introduction will be drafted by Chapin Cavender

• Section on non-Bragg diffraction is incomplete and will be drafted by Michael Wall’s postdoc (and former Mobley lab member) David Wych

• Plan for presenting experimental datasets in review article

  • For crystal datasets, is a PDB ID sufficient?

  • For NMR datasets, what metadata is desired?

OpenFF protein validation datasets

Chapin Cavender

Terminology

• Validation datasets are used to choose between models and should be quick to compute

• Test datasets are used to evaluate model performance and can be expensive to compute

Protein validation datasets

• QC datasets

  • Could use subset of TorsionDrives for molecules not used to train parameters

  • E.g. train on dipeptide TorsionDrives for all 26 sidechains, then use Ace-Val-X-Val-Nme tetrapeptides for validation

  • No additional infrastructure needs

• Experimental datasets

  • Crystal simulations are likely too expensive for validation, so focus on NMR observables for small peptides

    • ¹H, ¹³C, and ¹⁵N chemical shifts

    • ³J Scalar couplings

    • Residual dipolar couplings

    • NOESY intensities

  • Specific datasets are expected from LiveCoMS review

    • Cho dataset of blocked tripeptides (Ace-X-Y-Nme) from https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.24000

    • Beauchamp/Pande dataset of dipeptides, tripeptides, and tetraalanine from https://pubs.acs.org/doi/10.1021/ct2007814

  • Infrastructure needs - implement forward model in Evaluator or prepare input for external software?

• Kirkwood-Buff integrals

  • Datasets from Table 3 of https://pubs.acs.org/doi/10.1021/acs.jctc.1c00075

  • Infrastructure needs - calculation of pairwise radial distribution functions