title: Three-dimensional protein structure prediction: Methods and computational strategies.
abstract: A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction.
authors.affiliation: Federal University of Rio Grande do Sul, Institute of Informatics, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil. Electronic address: mdorn@inf.ufrgs.br.
authors.forename: Márcio
authors.initials: M
authors.lastname: Dorn
authors.affiliation: Federal University of Rio Grande do Sul, Center of Biotechnology, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil. Electronic address: mariel.barbachan@ufrgs.br.
authors.forename: Mariel Barbachan
authors.initials: MB
authors.lastname: E Silva
authors.affiliation: Federal University of Rio Grande do Sul, Institute of Informatics, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil. Electronic address: buriol@inf.ufrgs.br.
authors.forename: Luciana S
authors.initials: LS
authors.lastname: Buriol
authors.affiliation: Federal University of Rio Grande do Sul, Institute of Informatics, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil. Electronic address: lamb@inf.ufrgs.br.
authors.forename: Luis C
authors.initials: LC
authors.lastname: Lamb
keywords: Ab initio methods; Knowledge-based methods; Structural bioinformatics; Three-dimensional protein structure prediction