Cutoff lensing: predicting catalytic sites in enzymes.

ABSTRACT: Predicting function-related amino acids in proteins with unknown function or unknown allosteric binding sites in drug-targeted proteins is a task of paramount importance in molecular biomedicine. In this paper we introduce a simple, light and computationally inexpensive structure-based method to identify catalytic sites in enzymes. Our method, termed cutoff lensing, is a general procedure consisting in letting the cutoff used to build an elastic network model increase to large values. A validation of our method against a large database of annotated enzymes shows that optimal values of the cutoff exist such that three different structure-based indicators allow one to recover a maximum of the known catalytic sites. Interestingly, we find that the larger the structures the greater the predict

SUBMITTER: Aubailly S 

PROVIDER: S-EPMC4597221 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature