Massive Protein Structural Property Explorations Using New Indexing Mechanism

In order to comprehend residue environment, we use residue environmental sphere which is a sphere with 10 Å of radius, to describe environment information surrounding a residue. For the purpose of detecting residue-residue contacts more quickly and efficiently, we decompose a protein structure into lots of spheres, and it is a great challenge to store protein structure and sphere information in database. Therefore, we build a database for protein structure, ligand/substrate, and DNA/RNA information for quick search and mining to observe residue environment of protein structure. In each residue environmental sphere, we can easily identify neighbor residues and their properties, including secondary structure, physicochemical property, and bfactor, could be considered. In this paper, we focus on disulfide bond which stabilizes protein folding. Furthermore, we detect all possible residue contacts of cysteine pairs in three-dimensional space and disulfide bonds between two cysteines annotated in Protein Data Bank to analyze how disulfide bond affects protein structures. We use a sphere to represent a protein structure and build a database for protein structure and structure representation for further analysis.