Spatial Encoding Scheme for Protein Supporting Structure Discovery

• Main Authors: Yu-Feng Huang, Chia-Jui Yang, Yi-Wei Yang, Chien-Kang Huang
• Format: Conference Proceeding
• Language: English
• Subjects: Biochemistry; Bioinformatics; Biomedical engineering; Encoding; Heuristic algorithms; Iterative algorithms; Libraries; neighobrhood residues sphere; Oceans; Protein engineering; protein supporting structure discovery; spatial enconding scheme
• DOI: 10.1109/BIBE.2009.51

Protein function is highly correlated with its three dimensional conformation in order to interact with others proteins, ligands, substrates, inhibitors, etc. Studies on binding site and protein function have been investigated to understand the mechanism of protein activity; therefore, protein stability and flexibility play different roles on protein functions. In this work, we propose a framework to discover protein supporting structures, which employs the signatures of local structures and mines the rigid regions form the same/similar proteins.Through experiments and discussions, we heuristically determined the effective encoding method. Further we apply this encoding method in discovering protein supporting structure by identifying stable regions. Our results reveal that supporting structure can be discovered in selected enzyme families. Moreover, the reasons for supporting structure existence vary between protein families.