Protein Structure Comparison and Classifications into Domains

Protein structure classification by using bioinformatics can involve sequence similarity searches, multiple sequence alignment, characterization of domains, involuntary protein fold recognition and constructing three-dimensional models to atomic element. In this paper, a set of protocols to classify protein structure and sequence is presented. Structure classification systems, as applied for example in the SCOP, CATH, and FSSP databases, clarify the relationship between protein folds and function and inform on the evolution of protein domains. Proteins fold into three-D structures, and protein structures are more preserved than protein sequences. Therefore, given a protein structure, it is necessary to search for geometrically comparable proteins through protein structure evaluation. This is mostly done in circumstances where the resemblance at the sequence level is too minimal to be detected by any sequence-based similarity search program. The object of protein structure comparison is to get the largest structural similarity between two structures (Reed, 2011 P 139).