Hi, I am trying to train a predictor from some docking results. To do this I will need both true negative and true positive datasets. These datasets must have a PDB, small molecule and an indication of whether they interact.
I can probably make a true positive dataset by finding all PDBs which are bound to a small molecules but I'm not sure about the true negatives. I'm hoping that these datasets exist already from other publications.
Does anyone know where I might find these datasets? Thanks, Kevin
Most common method is to use DUD or newer version - DUDe. The generated compounds - called decoys, active compounds can be found in ChEMBL.
Dude! This tool is worthy of inclusion in CRAC: funny and/or weird names for bioinformatics tools
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