MCSS Fix and Update Docking parameters - Githubissues

drewnutt / open_combind

Open-source docking pipeline leveraging pairwise statistics

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MCSS Fix and Update Docking parameters #7

Closed drewnutt closed 1 year ago

drewnutt commented 1 year ago

Description

MCSS now sets all Halogens as the same AtomType like in the original ComBind paper.

Docking updated to have new atom types and set new default parameters

custom atom typing reduces the van der Waals radii of non-polar hydrogens and carbons to aid with large ligands fitting into a non-cognate receptor
default docking now uses --min_rmsd_filter=0

Added a util to count the number of poses in a *.sdf.gz file

Todos

Notable points that this PR has either accomplished or will accomplish.

[x] MCSS Merge Halogens
[x] Docking similar to Glide

Status

[ ] Ready to go