title: Contact pattern-induced pair potentials for protein fold recognition.
abstract: The protein structure prediction problem is considered as a problem of fitting a sequence into a folding motif. We focus on finding an approximative structure representation providing the best preferences or contact energies. A 2-D structure description in the form of specific contact matrices is used. The main features of our approach are (i) only contacts involved in characteristic interaction patterns are considered, (ii) amino acid pair preferences or contact energies related to these interaction patterns are derived from the structural database and (iii) from the evaluation of individual structure elements, hypotheses on the alignment of a new sequence to a given structure may be derived. Results are demonstrated in particular to examples of the blue copper proteins.
authors.affiliation: German National Research Center for Information Technology, Institute for Algorithms and Scientific Computing-Molecular Bioinformatics, Sankt Augustin.
authors.forename: J
authors.initials: J
authors.lastname: Selbig
mesh_terms: D001400:Azurin / Q000031:analogs & derivatives / Q000737:chemistry; D001665:Binding Sites; D006801:Humans; D008433:Mathematics; D008956:Models, Chemical; D015394:Molecular Structure; D009113:Muramidase / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012259:Ribonuclease, Pancreatic / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D011506:Proteins; C047163:pseudoazurin; D001400:Azurin; D012259:Ribonuclease, Pancreatic; D009113:Muramidase