A topological algorithm for identification of structural domains of proteins |
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Authors: | Frank Emmert-Streib Arcady Mushegian |
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Institution: | (1) Stowers Institute for Medical Research, 1000 E. 50th Street, MO 64110 Kansas City, USA;(2) University of Kansas Medical Center, KS 66160 Kansas City, USA;(3) University of Washington, 1705 NE Pacific St, Box 355065, WA 98195-5065 Seattle, USA |
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Abstract: | Background Identification of the structural domains of proteins is important for our understanding of the organizational principles and
mechanisms of protein folding, and for insights into protein function and evolution. Algorithmic methods of dissecting protein
of known structure into domains developed so far are based on an examination of multiple geometrical, physical and topological
features. Successful as many of these approaches are, they employ a lot of heuristics, and it is not clear whether they illuminate
any deep underlying principles of protein domain organization. Other well-performing domain dissection methods rely on comparative
sequence analysis. These methods are applicable to sequences with known and unknown structure alike, and their success highlights
a fundamental principle of protein modularity, but this does not directly improve our understanding of protein spatial structure. |
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