Paper Info
Title
Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction.
Abstract
The comparison of eight tools applicable to ligand-binding site prediction is presented. The methods examined cover three types of approaches: the geometrical (CASTp, PASS, Pocket-Finder), the physicochemical (Q-SiteFinder, FOD) and the knowledge-based (ConSurf, SuMo, WebFEATURE). The accuracy of predictions was measured in reference to the catalytic residues documented in the Catalytic Site Atlas. The test was performed on a set comprising selected chains of hydrolases. The results were analysed with regard to size, polarity, secondary structure, accessible solvent area of predicted sites as well as parameters commonly used in machine learning (F-measure, MCC). The relative accuracies of predictions are presented in the ROC space, allowing determination of the optimal methods by means of the ROC convex hull. Additionally the minimum expected cost analysis was performed. Both advantages and disadvantages of the eight methods are presented. Characterization of protein chains in respect to the level of difficulty in the active site prediction is introduced. The main reasons for failures are discussed. Overall, the best performance offers SuMo followed by FOD, while Pocket-Finder is the best method among the geometrical approaches.
Year
DOI
Venue
2011
10.1007/s10822-010-9402-0
Journal of computer-aided molecular design
Keywords
Field
DocType
Active site,Hydrolase,Ligand-binding site prediction,Receiver operating characteristic
Receiver operating characteristic,Ligand (biochemistry),Convex hull,Chemistry,Bioinformatics,Active site,Expected cost,Protein secondary structure,Optimal methods
Journal
Volume
Issue
ISSN
25
2
1573-4951
Citations 
PageRank 
References 
6
1.04
34
Authors
3
Name
Order
Citations
PageRank
Katarzyna Prymula1172.68
Tomasz Jadczyk2205.70
Irena Roterman37830.08