WONKAandOOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design
Open Access
- 24 February 2017
- journal article
- research article
- Published by International Union of Crystallography (IUCr) in Acta crystallographica. Section D, Structural biology
- Vol. 73 (3), 279-285
- https://doi.org/10.1107/s2059798316009529
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.OOMMPPAAhighlights 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/.Keywords
This publication has 18 references indexed in Scilit:
- WONKA: objective novel complex analysis for ensembles of protein–ligand structuresJournal of Computer-Aided Molecular Design, 2015
- OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural DataJournal of Chemical Information and Modeling, 2014
- QSAR Modeling: Where Have You Been? Where Are You Going To?Journal of Medicinal Chemistry, 2013
- Matched Molecular Pair Analysis in drug discoveryDrug Discovery Today, 2013
- Crystallographic Fragment ScreeningMethods in molecular biology (Clifton, N.J.), 2011
- Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemiaNature, 2011
- ChEMBL: a large-scale bioactivity database for drug discoveryNucleic Acids Research, 2011
- Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data SetsJournal of Chemical Information and Modeling, 2010
- The Problem of OverfittingJournal of Chemical Information and Computer Sciences, 2003
- Announcing the worldwide Protein Data BankNature Structural & Molecular Biology, 2003