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J Comput Aided Mol Des. 2015 Oct;29(10):963-73. doi: 10.1007/s10822-015-9866-z. Epub 2015 Sep 19.

WONKA: objective novel complex analysis for ensembles of protein-ligand structures.

Author information

  • 1SGC, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK.
  • 2Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 TG, UK.
  • 3Computational & Structural Chemistry, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
  • 4Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
  • 5Department of Biochemistry, University of Johannesburg, Aukland Park, 2006, South Africa.
  • 6SGC, 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.
  • 7Kennedy 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.

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.

KEYWORDS:

Bromodomains; Data driven drug design; Structure based drug design

PMID:
26387008
PMCID:
PMC4621702
DOI:
10.1007/s10822-015-9866-z
[PubMed - indexed for MEDLINE]
Free PMC Article
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