3DLigandSite: predicting ligand-binding sites using similar structures

Wass, Mark N. and Kelley, L. A. and Sternberg, M. J. E. (2010) 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Research, 38 . W469-W473. ISSN 0305-1048. (The full text of this publication is not available from this repository)

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Official URL
http://dx.doi.org/10.1093/nar/gkq406

Abstract

3DLigandSite is a web server for the prediction of ligand-binding sites. It is based upon successful manual methods used in the eighth round of the Critical Assessment of techniques for protein Structure Prediction (CASP8). 3DLigandSite utilizes protein-structure prediction to provide structural models for proteins that have not been solved. Ligands bound to structures similar to the query are superimposed onto the model and used to predict the binding site. In benchmarking against the CASP8 targets 3DLigandSite obtains a Matthew’s correlation co-efficient (MCC) of 0.64, and coverage and accuracy of 71 and 60%, respectively, similar results to our manual performance in CASP8. In further benchmarking using a large set of protein structures, 3DLigandSite obtains an MCC of 0.68. The web server enables users to submit either a query sequence or structure.

Item Type: Article
Additional information: Featured in supplement 2 of this volume.
Subjects: Q Science
Divisions: Faculties > Science Technology and Medical Studies > School of Biosciences
Depositing User: Mark Wass
Date Deposited: 09 Oct 2012 11:09
Last Modified: 07 Jun 2013 08:38
Resource URI: http://kar.kent.ac.uk/id/eprint/31433 (The current URI for this page, for reference purposes)
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