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IsoCleft Finder Interface paper has been published online
By: matthieu chartier  
May 1 2013


The NRG group has submitted a paper to the open access journal F1000 Research. The paper presents the web interface that uses our program IsoCleft for the detection of atomic similarities. The F1000 Research platform allows pre and post publication comments and reviews.

To access the article: http://f1000research.com/articles/2-117

To access the interface: http://bcb.med.usherbrooke.ca/isocleftfinder

Title
IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

Authors
Natalja Kurbatova (1), Matthieu Chartier (2), María Inés Zylber (2), Rafael Najmanovich (2)

Affiliations
(1) European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
(2) Department of Biochemistry, Université de Sherbrooke, Sherbrooke, J1H 5N4, Canada

Abstract
IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code) combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dataset using a cognate-similarity threshold. Local structural similarities are detected using the IsoCleft software and ranked according to two criteria (number of atoms in common and Tanimoto score of local structural similarity) and the associated Z-score and p-value measures of statistical significance. The results, including predicted ligands, target proteins, similarity scores, number of atoms in common, etc., are shown in a powerful interactive graphical interface. This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities. Similarities between top scoring ligands serve as an additional tool to judge the quality of the results obtained. We present several examples where IsoCleft Finder provides useful functional information. IsoCleft Finder results are complementary to existing approaches for the prediction of protein function from structure, rational drug design and x-ray crystallography. IsoCleft Finder can be found at: http://bcb.med.usherbrooke.ca/isocleftfinder.





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