Tutors
Sharon Bryan (Inte:Ligand), Jean-Christophe Mozziconacci (Schrödinger)
Software
- Inte:Ligand
- LigandScout (http://www.inteligand.com/ligandscout/)
- Schrödinger
- PhaseShape (http://www.schrodinger.com/products/14/34/)
- Phase (http://www.schrodinger.com/products/14/13/)
- Maestro (http://www.schrodinger.com/downloadcenter/10/)
Maestro can be downloaded for free for all academic users.
Datasets
The docking/pharmacophore dataset consists of 77 compounds: 11 active compounds and 66 decoys randomly selected from the QSAR classification dataset. Structures are provided with 3D coordinates in mol2 format in the file named P29274_docking-random.mol2. Of note, one of the active compounds and 8 of the decoys have an undefined chiral center, hence the two possible stereoisomers were included in the dataset. The named P29274_docking-random.mol2 thus contains 86 structures. The structure name allows one to distinguish active compounds ("chembl" prefix) from decoys ("pubchemdecoy" prefix).
In order to be able to compare individual results and prepared benchmarks, we advise you to use the PDB entry 3EML, which you can download from the PDB (http://www.rcsb.org).
Download: LigandScout supplementary files. A2A virtual screening results using LigandScout on 1 million commercially available compounds.
Download PhaseShape supplementary files
Instructions
- LigandScout tutorial (to be used with this dataset)
- Training videos are available for Glide and Maestro here
- PhaseShape tutorial