title: WONKA: objective novel complex analysis for ensembles of protein-ligand structures.
abstract: WONKA is a tool for the systematic analysis of an ensemble of protein-ligand structures. It makes the identification of conserved and unusual features within such an ensemble straightforward. WONKA uses an intuitive workflow to process structural co-ordinates. Ligand and protein features are summarised and then presented within an interactive web application. WONKA's power in consolidating and summarising large amounts of data is described through the analysis of three bromodomain datasets. Furthermore, and in contrast to many current methods, WONKA relates analysis to individual ligands, from which we find unusual and erroneous binding modes. Finally the use of WONKA as an annotation tool to share observations about structures is demonstrated. WONKA is freely available to download and install locally or can be used online at http://wonka.sgc.ox.ac.uk.
authors.affiliation: SGC, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK.|Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 TG, UK.
authors.forename: A R
authors.initials: AR
authors.lastname: Bradley
authors.affiliation: Computational & Structural Chemistry, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
authors.forename: I D
authors.initials: ID
authors.lastname: Wall
authors.affiliation: SGC, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK.|Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.|Department of Biochemistry, University of Johannesburg, Aukland Park, 2006, South Africa.
authors.forename: F
authors.initials: F
authors.lastname: von Delft
authors.affiliation: Computational & Structural Chemistry, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
authors.forename: D V S
authors.initials: DV
authors.lastname: Green
authors.affiliation: Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 TG, UK.
authors.forename: C M
authors.initials: CM
authors.lastname: Deane
authors.affiliation: SGC, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK. brian.marsden@sgc.ox.ac.uk.|Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, UK. brian.marsden@sgc.ox.ac.uk.
authors.forename: B D
authors.initials: BD
authors.lastname: Marsden
mesh_terms: D030562:Databases, Protein; D015195:Drug Design; D051548:Histone Acetyltransferases; D056488:Histone Chaperones; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D009687:Nuclear Proteins / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D035165:Transcription Factors, General; D057188:Workflow; D000092468:Bromodomain Containing Proteins
chemical_list: D051548:Histone Acetyltransferases; D056488:Histone Chaperones; D047908:Intracellular Signaling Peptides and Proteins; D008024:Ligands; D009687:Nuclear Proteins; D011506:Proteins; D035165:Transcription Factors, General; C000609272:BAZ2B protein, human; D000092468:Bromodomain Containing Proteins; C418612:PHIP protein, human; C402649:BRD1 protein, human
keywords: Bromodomains; Data driven drug design; Structure based drug design