Inferring boundary information of discontinuous-domain proteins.

Wetlaufer introduced the classification of domains into continuous and discontinuous. Continuous domains form from a single-chain segment and discontinuous domains are composed of two or more chain segments. Richardson identified approximately 100 domains in her review. Her assignment was based on the concepts that the domain would be independently stable and/or could undergo rigid-body-like movements with respect to the entire protein. There are now several instances where structurally similar domains occur in different proteins in the absence of noticeable sequence similarity. Possibly, the most notable of such domains is the trios-phosphate isomerase (TIM) barrel. With the increase in the number of known sequences, computer algorithms are required to identify the discontinuous domain of an unknown protein chain in order to determine its structure and function. We have developed a novel algorithm for discontinuous-domain boundary prediction based on a machine learning algorithm and interresidue contact interactions values. We have used 415 proteins, including 100 discontinuous-domain chains for training. There is no method available that is designed solely on a sequence based for the prediction of discontinuous domain. DomainDiscovery performed significantly well compared to the structure-based methods like structural classification of proteins (SCOP), class, architecture, topology and homologous superfamily (CATH), and DOMain MAKer (DOMAK).