3DLigandSite: predicting ligand-binding sites using similar structures

被引：483

作者：

Wass, Mark N. ^{[1
]}

Kelley, Lawrence A. ^{[1
]}

Sternberg, Michael J. E. ^{[1
]}

机构：

[1] Univ London Imperial Coll Sci Technol & Med, Ctr Bioinformat, Struct Bioinformat Grp, London SW7 2AZ, England

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

基金：

英国生物技术与生命科学研究理事会;

关键词：

IMPORTANT RESIDUES; PROTEIN-STRUCTURE; SEQUENCE; DATABASE;

D O I：

10.1093/nar/gkq406

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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. Predictions are visually displayed via an interactive Jmol applet. 3DLigandSite is available for use at http://www.sbg.bio.ic.ac.uk/3dligandsite.

引用

页码：W469 / W473

页数：5

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