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

ABSTRACT:

Motivation

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.

Results

We tested over 150 of the amino acid clustering schemes proposed in the literature with all-versus-all pairwise sequence alignments of sequences in the Distance mAtrix aLIgnment database. We combined several metrics from information

SUBMITTER: Peterson EL 

PROVIDER: S-EPMC2732308 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature