This thesis is about the identification of protein function from amino acid sequence and three-dimensional structure. Identification and prediction of protein functions are both essential components of our effort to understand the complexities of living systems. They also each play a critical role in the development of therapeutics. Protein function can be established in the laboratory using experimental methods, or it can be predicted using computational tools. Experimental determination of protein function is laborious and expensive. The process of annotation transfer is faster and more efficient, and it is therefore more used. Annotation is the process of naming the functions of proteins. Annotation transfer is the transfer of an assignment of function from one protein to another. Annotation transfer is based on homology which is established using computational tools for detecting sequence and/or structural similarities. Computational methods can also utilize the features of individual protein structures to predict function directly. In this thesis, computational methods are presented which have been designed to provide a better understanding of the assignment of protein function using protein sequence and structure information. Protein function analysis was performed using sequence and structure. In Chapter two, a quantitative relationship between protein sequence and function is presented using Pfam and G ene Ontology (GO) database. Results of this investigation can act as a guide for transfer of annotation using sequence homology. This investigation also provides an insight into the presence and propagation of erroneous annotations in the databases. Protein structure can also provide clues to protein function. In chapter 3, a computational method for generating a ligand in the active site of a protein with a known structure is presented. Physico-chemical properties of the active sites were utilized to predict ligands. Overall the results of this investigation provide a better understanding of protein function in living organisms.
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