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Extension of a local backbone description using a structural alphabet: A new approach to the sequence‐structure relationship
Author(s) -
de Brevern Alexandre G.,
Valadié Hélène,
Hazout Serge,
Etchebest Catherine
Publication year - 2002
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0220502
Subject(s) - extension (predicate logic) , alphabet , sequence (biology) , protein data bank , amino acid , probabilistic logic , computer science , algorithm , protein structure , simple (philosophy) , computational biology , biological system , chemistry , artificial intelligence , biology , biochemistry , philosophy , linguistics , programming language , epistemology
Protein Blocks (PBs) comprise a structural alphabet of 16 protein fragments, each 5 Cα long. They make it possible to approximate and correctly predict local protein three‐dimensional (3D) structures. We have selected the 72 most frequent sequences of five PBs, which we call Structural Words (SWs). Analysis of four different protein data banks shows that SWs cover 92% of the amino acids in them and provide a good structural approximation for residues (i.e., sequences) 9 Cα long. We present most of them in a simple network that describes 90% of the overall residues and, interestingly, includes more than 80% of the amino acids present in coils. Analysis of the network shows the specificity and quality of the 3D descriptions as well as a new type of relation between local folds and amino acid distribution. The results show that the 3D structure of these protein data banks can be easily described by a combination of subgraphs included in the network. Finally, a Bayesian probabilistic approach improved the prediction rate by 4%.