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Property‐based sequence representations do not adequately encode local protein folding information
Author(s) -
Solis A.D.,
Rackovsky S.
Publication year - 2007
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.21434
Subject(s) - encode , alphabet , folding (dsp implementation) , computer science , homology (biology) , property (philosophy) , computational biology , sequence (biology) , character (mathematics) , protein folding , theoretical computer science , mathematics , amino acid , biology , genetics , gene , biochemistry , engineering , linguistics , philosophy , geometry , epistemology , electrical engineering
We examine the informatic characteristics of amino acid representations based on physical properties. We demonstrate that sequences rewritten using contracted alphabets based on physical properties do not encode local folding information well. The best four‐character alphabet can only encode ∼57% of the maximum possible amount of structural information. This result suggests that property‐based representations that operate on a local length scale are not likely to be useful in homology searches and fold‐recognition exercises. Proteins 2007. © 2007 Wiley‐Liss, Inc.