Prediction and Classification for GPCR Sequences Based on Ligand Specific Features

  • Bekir Ergüner
  • Özgün Erdoğan
  • Uğur Sezerman
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4263)

Abstract

Functional identification of G-Protein Coupled Receptors (GPCRs) is one of the current focus areas of pharmaceutical research. Although thousands of GPCR sequences are known, many of them are orphan sequences (the activating ligand is unknown). Therefore, classification methods for automated characterization of orphan GPCRs are imperative. In this study, for predicting Level 1 subfamilies of GPCRs, a novel method for obtaining class specific features, based on the existence of activating ligand specific patterns, has been developed and utilized for a majority voting classification. Exploiting the fact that there is a non-promiscuous relationship between the specific binding of GPCRs into their ligands and their functional classification, our method classifies Level 1 subfamilies of GPCRs with a high predictive accuracy between 99% and 87% in a three-fold cross validation test. The method also tells us which motifs are significant for class determination which has important design implications. The presented machine learning approach, bridges the gulf between the excess amount of GPCR sequence data and their poor functional characterization.

Keywords

G-Protein Coupled Receptors (GPCRs) ligand specificity GPCR sequence 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Bekir Ergüner
    • 1
  • Özgün Erdoğan
    • 1
  • Uğur Sezerman
    • 1
  1. 1.Biological Sciences and BioengineeringSabanci UniversityIstanbulTurkey

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