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The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool

  • Maksim Kouza
  • Eshel Faraggi
  • Andrzej Kolinski
  • Andrzej KloczkowskiEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1484)

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 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 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.

Key words

Secondary structure prediction GOR Information theory Protein aggregation 

Notes

Acknowledgments

A. Kloczkowski would like to acknowledge support provided by start-up funds from The Research Institute of Nationwide Children’s Hospital. This work was also supported by the Polish Ministry of Science and Higher Education Grant No. IP2012 016872 and “Mobilnosc Plus” No. DN/MOB/069/IV/2015; the National Science Center grant [MAESTRO 2014/14/A/ST6/00088].

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Maksim Kouza
    • 1
  • Eshel Faraggi
    • 2
    • 5
  • Andrzej Kolinski
    • 1
  • Andrzej Kloczkowski
    • 3
    • 4
    Email author
  1. 1.Faculty of ChemistryUniversity of WarsawWarsawPoland
  2. 2.Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisUSA
  3. 3.Battelle Center for MathematicalMedicineNationwide Children’s HospitalColumbusUSA
  4. 4.Department of PediatricsThe Ohio State University College of MedicineColumbusUSA
  5. 5.Research and Information Systems, LLCIndianapolisUSA

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