This page provides ligand library with multiple conformations, holo form PDB file, and apo structure PDB file.
This dataset was used as a benchmark set in following paper: "PatchSurfers: Programs for Local Molecular Property-Based Binding Ligand Prediction" Woong-Hee Shin, Mark Gregory Bures, and Daisuke Kihara, Methods, Submitted.
Selected ten ligands from DUD set (dud.docking.org). All the datasets were downloaded in mol2 format. In this benchmark set, multiple conformations (up to 50) of ligands were generated by OpenEye OMEGA and provided in PDB format. OMEGA parameters were set to '-ewindow 15.0 -maxconfs 50 -rmsrange "0.5,0.8,1.0" -rangeIncrement 5'.
Each target is compressed as a '.tar.gz' file. 'target' folder contains holo receptor structure, its cognate ligand, and apo receptor structure in PDB format. The ligands in 'actives' directory are known active ligands, while those in 'decoys' directory are decoy molecules have similar chemical properties to the active compounds.
If you have any questions or suggestions, please feel free to contact us (dkihara@purdue.edu).