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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/.

Original publication

DOI

10.1107/s2059798316009529

Type

Journal article

Journal

Acta crystallographica. Section D, Structural biology

Publication Date

03/2017

Volume

73

Pages

279 - 285

Addresses

Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles, Oxford OX1 3LB, England.

Keywords

Humans, Proteins, Ligands, Binding Sites, Protein Binding, Structure-Activity Relationship, Drug Design, Computer-Aided Design, Software, Databases, Protein, Molecular Docking Simulation