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Protein topology from predicted residue contacts
Author(s) -
Taylor William R.,
Jones David T.,
Sadowski Michael I.
Publication year - 2012
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 - 10.1002/pro.2002
Subject(s) - sequence (biology) , consistency (knowledge bases) , residue (chemistry) , topology (electrical circuits) , protein structure , computational biology , multiple sequence alignment , sequence alignment , computer science , physics , statistical physics , biological system , chemistry , mathematics , peptide sequence , combinatorics , biology , genetics , gene , artificial intelligence , biochemistry
Residue contacts predicted from correlated positions in a multiple sequence alignment are often sparse and uncertain. To some extent, these limitations in the data can be overcome by grouping the contacts by secondary structure elements and enumerating the possible packing arrangements of these elements in a combinatorial manner. Strong interactions appear frequently but inconsistent interactions are down‐weighted and missing interactions up‐weighted. The resulting improved consistency in the predicted interactions has allowed the method to be successfully applied to proteins up to 200 residues in length which is larger than any structure previously predicted using sequence data alone.