Construction of an Integrated Environment for Sequence, Structure, Property and Function Analysis of Proteins

Abstract

One of the most important goals in molecular biology is to elucidate the relationship among sequence, structure, function and properties of biomolecules. Such knowledge would enable us to design the modifications of biomolecules for particular functions, and drugs to modify the function and property of biomolecules. Now, the number of entries in the Protein Data Bank (PDB) is over 10,000. These prized structural data should be used to understand the molecular mechanism of structural integrity and stability of biomolecules. The functionally important sites such as active sites in enzyme and ligand binding sites tend to be conserved among a family of proteins. The conserved amino acid sequences are called motif, and many motifs have been known so far. The physico-chemical properties of biomolecules are studied by various biophysical and biochemical methods. The structure, function and property of biomolecules are often closely related, but it is usually difficult to infer the relation from individual data. Thus, if researchers are interested in the structure of particular molecules and its relationship with function and physico-chemical properties, they usually need to examine several databases and literatures to obtain the information of their interest. On the other hand, structure comparison is one of the most important and interesting subject of bioinformatics because it plays a key role in structure classification, structure search, motif detection, function prediction, and so on. It would be useful to have an integrated environment where one can examine the relationship among sequence, structure, function and property of biomolecules based on databases and a lot of search, analysis and visualization tools.