Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions

The GOR Method of Protein Secondary Structure Prediction, and its Application as Protein Aggregation Prediction Tool

Source:

Methods in Molecular Biology, 1484:7-24, 2017

Abstract

The GOR method of protein secondary structure prediction is described. The original method was published by Garnier, Osguthorpe and Robson in 1978, and was one of the first successful methods to predict protein secondary structure from amino acid sequence. The method is based on the information theory, and an assumption that information function of a protein chain can be approximated by a sum of information from single residues and pairs of residues. The analysis of frequencies of occurrence of secondary structure for singlets and doublets of residues in a protein database enables prediction of secondary structure for new amino acid sequences. Because of these simple physical assumptions the GOR method has a conceptual advantage over other later developed methods such as PHD, PSIPRED and others, that are based on Machine Learning methods (like Neural Networks), give slightly better predictions, but have a “black box” nature. The GOR method has been continuously improved and modified for 30 years with the last GOR V version published in 2002, and the GOR V server developed in 2005. We discuss here the original GOR method and the GOR V program and the web server. Additionally we discuss new highly interesting and important applications of the the GOR method to chameleon sequences in protein folding simulations, and for prediction of protein aggregation propensities. Our preliminary studies show that the GOR method is a promising and efficient alternative to other protein aggregation predicting tools. This shows that the GOR method despite being almost 40 years old is still important and has significant potential in application to new scientific problems.