The Study on Local Structure Representation and Local Conserved Structure Discovery

Local region conservation has been studied for many years because biologists believe that local conservation could be highly related to protein functions. The concept of local region conservation comes from a motif, a fragment with biological or functional meaning. Besides, structure-based identification of homologues often succeeds where sequence-alone-based methods fail, because in many cases evolution retains the folding pattern long after sequence similarity becomes undetectable. Thus, prediction of protein function from sequence and structure is a difficult problem, because homologous proteins often have different functions. Alternative methods include inferring conservation patterns in members of a functionally uncharacterized family for which many sequences and structures are known. The researches show that sequence conservation could be discovered that their corresponding residues in 3D space are a compact region and close to ligand. But the question is that is it possible to discover compact regions via protein structure analysis; therefore, our motivation is find out a local structure representation and apply the concept of mining frequent item set to discover local structure conservation. In the experiments, we use enzyme classification to discover local structure conservations, which we can easily identify the connection linked by detected local structure conservations and substrates.