Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns.

ABSTRACT:

Background

The three-dimensional structure of a protein is an essential aspect of its functionality. Despite the large diversity in protein structures and functionality, it is known that there are common patterns and preferences in the contacts between amino acid residues, or between residues and other biomolecules, such as DNA. The discovery and characterization of these patterns is an important research topic within structural biology as it can give fundamental insight into protein structures and can aid in the prediction of unknown structures.

Results

Here we apply an efficient spatial pattern miner to search for sets of amino acids that occur frequently in close spatial proximity in the protein structures of the Protein DataBank. This allowed us to mine for a new class o

SUBMITTER: Meysman P 

PROVIDER: S-EPMC4318390 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature