A tool for protein substructure matching against a database of protein tertiary structure

Proteins are large macromolecules that carry out most cellular activities and obtaining more information about them with minimum cost is requested by researchers. Financial and time costs of experimental works and massive amount of data available nowadays make it necessary to develop and use computer software to analyze the data. There are several tools available to search a substructure in a protein or in a database of proteins with different purposes. Each one of these tools has its own advantages and limitations. In this research, we have developed a comprehensive and new tool to tackle the weaknesses of other tools and to present a broad application to the users. The tool presented here is aimed to search a substructure of a protein in a database of proteins obtained from Protein Data Bank (PDB) [1]. The structure could be already known, a completely new protein or an alternation of a protein. To diminish the computational cost of this program, we have reduced protein structures to their equivalent graph and then we have used a subgraph matching algorithm to find proteins in the database containing any desired protein substructure.

کلیدواژه ها:

Protein structure ، Protein data bank ، Graph matching ، Protein search engine