Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment | Zendy

Eric L. Peterson | Zendy; Jané Kondev | Zendy; Julie A. Theriot | Zendy; Rob Phillips | Zendy

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Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment

Author(s) -

Eric L. Peterson,

Jané Kondev,

Julie A. Theriot,

Rob Phillips

Publication year - 2009

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btp164

Subject(s) - pairwise comparison , computer science , similarity (geometry) , cluster analysis , contrast (vision) , alphabet , algorithm , sequence alignment , sensitivity (control systems) , pattern recognition (psychology) , mathematics , artificial intelligence , peptide sequence , biology , genetics , gene , philosophy , linguistics , electronic engineering , engineering , image (mathematics)

Many proteins with vastly dissimilar sequences are found to share a common fold, as evidenced in the wealth of structures now available in the Protein Data Bank. One idea that has found success in various applications is the concept of a reduced amino acid alphabet, wherein similar amino acids are clustered together. Given the structural similarity exhibited by many apparently dissimilar sequences, we undertook this study looking for improvements in fold recognition by comparing protein sequences written in a reduced alphabet.

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