GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model.
We describe a novel system, GRIFFIN (G-protein and Receptor Interaction Feature Finding INstrument), that predicts G-protein coupled receptor (GPCR) and G-protein coupling selectivity based on a support vector machine (SVM) and a hidden Markov model (HMM) with high sensitivity and specificity. Based on our assumption that whole structural segments of ligands, GPCRs and G-proteins are essential to determine GPCR and G-protein coupling, various quantitative features were selected for ligands, GPCRs and G-protein complex structures, and those parameters that are the most effective in selecting G-protein type were used as feature vectors in the SVM. The main part of GRIFFIN includes a hierarchical SVM classifier using the feature vectors, which is useful for Class A GPCRs, the major family. For the opsins and olfactory subfamilies of Class A and other minor families (Classes B, C, frizzled and smoothened), the binding G-protein is predicted with high accuracy using the HMM. Applying this system to known GPCR sequences, each binding G-protein is predicted with high sensitivity and specificity (>85% on average). GRIFFIN (http://griffin.cbrc.jp/) is freely available and allows users to easily execute this reliable prediction of G-proteins.
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.
Yukimitsu
Y
Yabuki
Takahiko
T
Muramatsu
Takatsugu
T
Hirokawa
Hidehito
H
Mukai
Makiko
M
Suwa
D001185:Artificial Intelligence; D020962:Heterotrimeric GTP-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D020407:Internet; D008024:Ligands; D008390:Markov Chains; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D020539:Sequence Analysis, Protein; D012984:Software
D008024:Ligands; D043562:Receptors, G-Protein-Coupled; D020962:Heterotrimeric GTP-Binding Proteins