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A new catalog of protein β‐sheets
Author(s) -
Parisien Marc,
Major François
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20677
Subject(s) - spider , folding (dsp implementation) , annotation , computer science , computational biology , protein folding , domain (mathematical analysis) , set (abstract data type) , polypeptide chain , protein structure , structural motif , crystallography , structural alignment , chemistry , amino acid , biology , peptide sequence , artificial intelligence , biochemistry , mathematics , sequence alignment , engineering , programming language , structural engineering , zoology , mathematical analysis , gene
Systematic protein folding studies depend on protein three‐dimensional structure annotation, the assignment of amino acid structural types from atomic coordinates. Significant stabilizing factors between adjacent β‐sheet peptide chains have recently been characterized and were not considered during the development of previously published annotation methods. To produce an accurate β‐sheet domain catalog and to encompass the full β‐sheet spectacle, we developed a method, β‐Spider, which evaluates a packing energy between adjacent peptide chains in accordance with the newly discovered stabilizing factors. While considering important energetic factors, our approach also minimizes the use of subjective criteria, such as (ϕ,ψ) boundaries and sets of H‐bonding motifs that are used in other existing methods. As a result of the application of β‐Spider to a set of available high‐resolution X‐ray crystal structures, we present here a new β‐sheet catalog that differs considerably from the one produced by the most acclaimed DSSP method. The catalog includes new H‐bonding motifs that were never reported. Proteins 2005. © 2005 Wiley‐Liss, Inc.