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drewnutt / open_combind

Open-source docking pipeline leveraging pairwise statistics
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Protonation and Alignment #13

Closed drewnutt closed 1 year ago

drewnutt commented 1 year ago

Description

Using OpenMM/PDBFixer the receptor is protonated and the hydrogens are minimized. This allows us to detect H-bond donors on the protein using the current featurization algorithm.

This also adds steps to ensure alignment of the protein structures are occurring between the chains that the ground truth ligand is docked to. We find the chain with the largest amount of atoms near the ligand and align the atoms within 15 A of the ligand on that chain.

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

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drewnutt commented 1 year ago

Will leave this CI failing, need to figure out why pdbfixer won't install.