title: WONKA and OOMMPPAA: analysis of protein-ligand interaction data to direct structure-based drug design.
abstract: 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/.
authors.affiliation: Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles, Oxford OX1 3LB, England.
authors.forename: Charlotte M
authors.initials: CM
authors.lastname: Deane
authors.affiliation: Computational and Structural Chemistry, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England.
authors.forename: Ian D
authors.initials: ID
authors.lastname: Wall
authors.affiliation: Computational and Structural Chemistry, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England.
authors.forename: Darren V S
authors.initials: DV
authors.lastname: Green
authors.affiliation: SGC, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, England.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Marsden
authors.affiliation: Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles, Oxford OX1 3LB, England.
authors.forename: Anthony R
authors.initials: AR
authors.lastname: Bradley
mesh_terms: D001665:Binding Sites; D017076:Computer-Aided Design; D030562:Databases, Protein; D015195:Drug Design; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D008024:Ligands; D011506:Proteins
keywords: OOMMPPAA; WONKA; computational chemistry; structure-based drug design