Geon Tae Ahn , Hyeong Seok Yoon , Eui Yoon Hwang , Jin Hong Kim , Myung Joon Lee

The KIPS Transactions:PartD, Vol. 10, No. 1, pp. 133-142, Feb. 2003
10.3745/KIPSTD.2003.10.1.133,   PDF Download:

Abstract

The major challenge for post-genomic study is to identify structural similarity and relationships of proteins. SCOP (Structural Classification Of Proteins) is a typical database for this purpose, providing a detailed description of the structural and functional relationships of the proteins whose three-dimensional structures have been determined. Unfortunately, since the SCOP data is only available as a plain text format, it is cumbersome and error-prone to develop tools and resources for the different kinds of analysis of the data. Therefore it is desirable to provide the data in a standard structured format, allowing researchers to utilize the data more effectively. To meet these requirements, we have developed an XML representation for the SCOP data, named SCOPML and the translator to convert the SCOP data into the associated SCOPML documents. Also, we have implemented a browsing tool, named SCOPBrowser, for effective search of SCOP database. In addition to the information available from the SCOP site, users of the tool can obtain various information such as viewing the tree hierarchy of structure classification of proteins, searching into whole protein domains, showing XML contents of a specific domain, and some useful statistics about protein structures.

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