openforcefield/protein-ligand-benchmark

Choice of ligands in the repo

Opened this issue · 2 comments

annamherz commented

Hello! I'm going to be running a benchmark with the p38, mcl1 and tyk2 ligands. Looking at the ligands available in this repo, I've noticed that some of the ligands are not included when compared to those included in the JACS 2015 benchmark paper, and I was wondering why? I've read through section 4.2 in the paper but was wondering if there was more specific documentation for why each specific ligand that was not included was omitted in this repo?

Thank you!

nonsensejoke commented

For MCL1 system, the ligands which are missing SDF in this repo have aromatic ring that can take two conformations. I guess this could complicates the FEP simulation.

ijpulidos commented

Apologies for such a late response on this. You are correct at pointing out that the ligands in the repo don't correspond exactly to the ones in the JACS paper. For that we suggest you use the release 0.2.1.

The reason that these ligands are now not in the dataset is because we have detected some issues with them. The discussion around it can be seen in #52 if that helps.