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openforcefield / protein-ligand-benchmark

Protein-Ligand Benchmark Dataset for Free Energy Calculations
MIT License
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MCL-1 is not capped at C terminus? #75

Closed IAlibay closed 1 year ago

IAlibay commented 2 years ago

Linked to #68, MCL-1 does not have a cap at the C terminus even though 4HW3 states that the protein is missing residues 322 and 323.

Is this intentional?

IAlibay commented 2 years ago

pinging @bobym

bobym commented 2 years ago

Looking back at my notes, this stems from a misunderstanding of the assay protocol. The authors assayed the ligands using an MCL1 construct that had the last 5 AA deleted. I misread the residues in the 4WH3 structure and thought the missing residues were a part of that deletion because the numbering in their SI and the PDB are different. Opening a PR to fix this now.

ijpulidos commented 1 year ago

This has been solved via #82