Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database.

ABSTRACT:

Background

Identifying protein functional sites (PFSs) and, particularly, the physicochemical interactions at these sites is critical to understanding protein functions and the biochemical reactions involved. Several knowledge-based methods have been developed for the prediction of PFSs; however, accurate methods for predicting the physicochemical interactions associated with PFSs are still lacking.

Results

In this paper, we present a sequence-based method for the prediction of physicochemical interactions at PFSs. The method is based on a functional site and physicochemical interaction-annotated domain profile database, called fiDPD, which was built using protein domains found in the Protein Data Bank. This method was applied to 13 target proteins from the very recent Criti

SUBMITTER: Han M 

PROVIDER: S-EPMC5984826 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature