CCL: PharmBench v1.0 Community Benchmarking Dataset

 Sent to CCL by: Simon Cross [simon],[moldiscovery.com]
 Dear Colleagues,
We would like to draw your attention to the publication of the PharmBench 1.0 dataset for the evaluation of molecular alignment and pharmacophore elucidation approaches.
The dataset consists of 81 targets, containing 960 ligands in total. The dataset is based on known pharmaceutically relevant co-crystallised protein ligand complexes, which were filtered to leave high-resolution structures containing drug-like small molecule ligands, for which electron density is also available at the EDS server. For each target the structures have been aligned using the receptor backbone atoms, and then the ligands extracted and prepared by fixing their atom types and adding hydrogen atoms.
The datasets therefore contain target ligands, aligned in the biologically relevant frame of reference, to act as a 'gold standard' reference set. The two-dimensional structures of these ligands are also provided.
An ideal molecular alignment or pharmacophore elucidation method should be able to read the two-dimensional input structures, and output three-dimensional alignments of the ligands that are equivalent to the gold standard alignments. In the coming weeks a web service will be set up to enable user-provided alignment models to be evaluated using the same approach as described in the publication (dx.doi.org/10.1021/ci300154n). 
 The dataset is available at pharmbench.moldiscovery.com.
 Kind regards,
 Simon
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 Dr. Simon Cross
 Snr Scientist & Product Manager
 Molecular Discovery Ltd
 simon[at]moldiscovery[dot]com
 +44 7980 572278