title: The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool.
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.
authors: Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland.
authors: Maksim
authors: M
authors: Kouza
authors: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46032, USA.|Research and Information Systems, LLC, Indianapolis, Indiana, USA.
authors: Eshel
authors: E
authors: Faraggi
authors: Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland.
authors: Andrzej
authors: A
authors: Kolinski
authors: Battelle Center for MathematicalMedicine, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43215, USA. Andrzej.Kloczkowski@nationwidechildrens.org.|Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA. Andrzej.Kloczkowski@nationwidechildrens.org.
authors: Andrzej
authors: A
authors: Kloczkowski
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D030562:Databases, Protein; D066329:Protein Aggregates / Q000235:genetics*; D017510:Protein Folding; D017433:Protein Structure, Secondary / Q000235:genetics*; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D066329:Protein Aggregates; D011506:Proteins
keywords: GOR; Information theory; Protein aggregation; Secondary structure prediction