| Summary: | 碩士 === 國立交通大學 === 資訊科學與工程研究所 === 97 === In protein science, the common belief is that amino acid sequence determines protein structure, and then protein structure determines the biological function. As the availability of the rapidly growing number of protein crystal structures and the advent of proteomics technologies, many methods have been proposed to identify sequence-structure-function relationships.
In this study, we investigate the relationship of protein sequence-structure-function by surveying PROSITE database. PROSITE is a widely used database that maintains annotated biological motifs. We review the structurally conserved property of PROSITE patterns to validate the fundamental principle-protein structure leads to protein function.
In addition, we proposed fastCOPS that integrates a quick screening method, 3D-BLAST, an accurate structural alignment method, MAMMOTH, and the mechanism of recursive truncation with an appropriate logic flow. In general, tools and methods currently available can be adopted in the fastCOPS framework as long as they are compatible with the design. The quick component should be able to accept a protein fragment as input, and the accurate component has to be capable of aligning partial structures with possible gap insertions.
We apply fastCOPS to achieve the task of structural motif search and identification. The fastCOPS has been evaluated on various structural motifs, including the treble clef finger motif, and the leucine-rich repeat motif. In addition, we use a PROSITE pattern as query to demonstrate the capability that fastCOPS can find structurally conserved
fragments but using sequence alignment tool will hardly be achieved.
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