Property-based sequence representations do not adequately encode local protein folding information.
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 approximately 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.
Solis
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AD
Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, USA.
Rackovsky
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S
D000595:Amino Acid Sequence; D016000:Cluster Analysis; D008969:Molecular Sequence Data; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
D011506:Proteins