Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues.

ABSTRACT: Enzymes play a fundamental role in almost all biological processes and identification of catalytic residues is a crucial step for deciphering the biological functions and understanding the underlying catalytic mechanisms. In this work, we developed a novel structural feature called MEDscore to identify catalytic residues, which integrated the microenvironment (ME) and geometrical properties of amino acid residues. Firstly, we converted a residue's ME into a series of spatially neighboring residue pairs, whose likelihood of being located in a catalytic ME was deduced from a benchmark enzyme dataset. We then calculated an ME-based score, termed as MEscore, by summing up the likelihood of all residue pairs. Secondly, we defined a parameter called Dscore to measure the relative distance of a r

SUBMITTER: Han L 

PROVIDER: S-EPMC3400608 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature