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PKUGaoGroup / DSDP

Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.
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Suggestion: A convenient interface for HTVS #7

Open pikakolendo02 opened 9 months ago

pikakolendo02 commented 9 months ago

The current version requires:

For each complex you want to predict, you need a directory containing the ligand and protein file. For example:

DSDP_dataset
└───name1
    │   name1_protein.pdbqt
    │   name1_ligand.pdbqt
└───name2
    │   name2_protein.pdbqt
    │   name2_ligand.pdbqt
...

which could be not convenient for HTVS. For example, I have 1 protein and 10000 ligands, thus I should create 10000 folders and each folder has the same protein (or symlink?). A convenient interface that allows docking a list of one target with many ligands (or 1 ligand with many targets, for reverse docking) is better, in my opinion.

biocheming commented 8 months ago

Just insert a loop in the main() function