Biology Reference
In-Depth Information
Chapter 4
Comparative Analysis of Techniques
Oriented on the Recognition of Ligand
Binding Area in Proteins
Paweł Alejster , Mateusz Banach , Wiktor Jurkowski , Damian Marchewka,
and Irena Roterman-Konieczna
Keywords
Geometric analysis Knowledge mining F-measure MCC ROC
curve Precision Recall True positive False positive True negative False nega-
tive Sensitivity Comparative analysis Receiver operating characteristic False
positive rate True positive rate CASTp Pocket- fi nder QSite- fi nder SuMo
ConSurf Computed atlas of surface topography of proteins Conservative residues
SuMo - surfing the molecules Target protein Easy proteins Hard proteins
Fuzzy oil drop
4.1
Introduction
This chapter presents an analysis of the various models implemented by software
packages which enable computerized identification of ligand binding sites.
In general, two distinct classes of models can be defined: those which rely on
geometric analysis of binding pockets (CASTp, Q-Site-Finder, Pocket-Finder) and
those based on knowledge mining (SuMo, ConSurf and the “fuzzy oil drop” model).
P. Alejster M. Banach D. Marchewka I. Roterman-Konieczna (
*
)
Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College,
Lazarza 16 , 31-530 Cracow , Poland
e-mail: myroterm@cyf-kr.edu.pl
Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University,
Reymonta 4 , 30-059 Cracow , Poland
W. Jurkowski (
*
)
Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of
Luxembourg, Campus Belval 7, avenue des Hauts-Fourneaux, Esch-Belval, L 4362, Luxembourg
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