title: ProCoCoA: A quantitative approach for analyzing protein core composition.
abstract: Defining the amino acid composition of protein cores is fundamental for understanding protein folding, as different architectures might achieve structural stability only in the presence of specific amino acid networks. Quantitative characterization of protein cores in relation to the corresponding structures and dynamics is needed to increase the reliability of protein engineering procedures. Unambiguous criteria based on atom depth considerations were established to assign amino acid residues to protein cores and, hence, for classifying inner and outer molecular moieties. These criteria were summarized in a new tool named ProCoCoA, Protein Core Composition Analyzer. An user-friendly web interface was developed, available at the URL: http://www.sbl.unisi.it/prococoa. An accurate estimate of protein core composition for six protein architectures selected from the CATH database of solved structures has been carried out, and the obtained results indicate the presence of specific patterns of amino acid core composition in different protein folds.
authors: Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy. bottini4@unisi.it
authors: Silvia
authors: S
authors: Bottini
authors: Andrea
authors: A
authors: Bernini
authors: Matteo
authors: M
authors: De Chiara
authors: Diego
authors: D
authors: Garlaschelli
authors: Ottavia
authors: O
authors: Spiga
authors: Marco
authors: M
authors: Dioguardi
authors: Elisa
authors: E
authors: Vannuccini
authors: Anna
authors: A
authors: Tramontano
authors: Neri
authors: N
authors: Niccolai
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins