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WONKA and OOMMPPAA : analysis of protein–ligand interaction data to direct structure‐based drug design
Author(s) -
Deane Charlotte M.,
Wall Ian D.,
Green Darren V. S.,
Marsden Brian D.,
Bradley Anthony R.
Publication year - 2017
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.374
H-Index - 138
ISSN - 2059-7983
DOI - 10.1107/s2059798316009529
Subject(s) - protein ligand , chembl , computational biology , computer science , context (archaeology) , protein data bank (rcsb pdb) , protein data bank , ligand (biochemistry) , drug discovery , protein structure , chemistry , bioinformatics , biology , stereochemistry , biochemistry , receptor , paleontology
In this work, two freely available web-based interactive computational tools that facilitate the analysis and interpretation of protein-ligand interaction data are described. Firstly, WONKA, which assists in uncovering interesting and unusual features (for example residue motions) within ensembles of protein-ligand structures and enables the facile sharing of observations between scientists. Secondly, OOMMPPAA, which incorporates protein-ligand activity data with protein-ligand structural data using three-dimensional matched molecular pairs. OOMMPPAA highlights nuanced structure-activity relationships (SAR) and summarizes available protein-ligand activity data in the protein context. In this paper, the background that led to the development of both tools is described. Their implementation is outlined and their utility using in-house Structural Genomics Consortium (SGC) data sets and openly available data from the PDB and ChEMBL is described. Both tools are freely available to use and download at http://wonka.sgc.ox.ac.uk/WONKA/ and http://oommppaa.sgc.ox.ac.uk/OOMMPPAA/.