Review of QSAR models for enzyme classes of drug targets: Theoretical background and applications in parasites, hosts, and other organisms.
The number of protein 3D structures without function annotation in Protein Data Bank (PDB) has been steadily increased. Many of these proteins are relevant for Pharmaceutical Design because they may be enzymes of different classes that could become drug targets. This fact has led in turn to an increment of demand for theoretical models to give a quick characterization of these proteins. In this work, we present a review and discussion of Alignment-Free Methods (AFMs) for fast prediction of the Enzyme Classification (EC) number from structural patterns. We referred to both methods based on linear techniques such as Linear Discriminant Analysis (LDA) and/or non-linear models like Artificial Neural Networks (ANN) or Support Vector Machine (SVM) in order to compare linear vs. non-linear classifiers. We also detected which of these models have been implemented as Web Servers free to the public and compiled a list of some of these web sites. For instance, we reviewed the servers implemented at portal Bio-AIMS (http://miaja.tic.udc.es/Bio-AIMS/EnzClassPred.php) and the server EzyPred (http://www.csbio.sjtu.edu.cn/bioinf/EzyPred/).
Concu
Riccardo
R
Department of Microbiology and Parasitology, University of Santiago de Compostela, Spain.
Podda
Gianni
G
Ubeira
Florencio M
FM
González-Díaz
Humberto
H
D000818:Animals; D003198:Computer Simulation; D017076:Computer-Aided Design; D030562:Databases, Protein; D015195:Drug Design; D004798:Enzymes / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism; D006801:Humans; D007091:Image Processing, Computer-Assisted; D020407:Internet; D008968:Molecular Conformation; D058990:Molecular Targeted Therapy; D010271:Parasites / Q000187:drug effects*; D010272:Parasitic Diseases / Q000188:drug therapy*; D011487:Protein Conformation; D021281:Quantitative Structure-Activity Relationship; D020539:Sequence Analysis, Protein; D012984:Software
D004798:Enzymes