TAILIEUCHUNG - SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures

The database community has insulated itself from the information retrieval community, and has largely eschewed dealing with messy data types like time and space (not everyone has, just most of us.) We had our hands full dealing with the “simple stuff” of numbers, strings, and relational operators on them. But, real ap- plications have massive amounts of text data, have temporal prop- erties, and have spatial properties. The DBMS extensibility offered by integrating languages with the DBMS makes it relatively easy to add data types. | JMB MS 422 Cust. Ret. No. CAM 502 94 SGML J. Mol. Biol. 1995 247 536-540 JMB Communication SCOP A Structural Classification of Proteins Database for the Investigation of Sequences and Structures Alexey G. Murzin Steven E. Brenner Tim Hubbard and Cyrus Chothia MRC Laboratory of Molecular Biology and Cambridge Centre for Protein Engineering Hills Road Cambridge CB2 2QH England Corresponding author To facilitate understanding of and access to the information available for protein structures we have constructed the Structural Classification of Proteins scop database. This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. It also provides for each entry links to co-ordinates images of the structure interactive viewers sequence data and literature references. Two search facilities are available. The homology search permits users to enter a sequence and obtain a list of any structures to which it has significant levels of sequence similarity. The key word search finds for a word entered by the user matches from both the text of the scop database and the headers of Brookhaven Protein Databank structure files. The database is freely accessible on World Wide Web WWW with an entry point to URL http scop scop an old English poet or minstrel Oxford English Dictionary cron pile accumulation Russian Dictionary . Keywords protein families superfamilies folds evolutionary relationships Nearly all proteins have structural similarities with other proteins and in many cases share a common evolutionary origin. The knowledge of these relationships makes imp ortant contributions to molecular biology and to other related areas of science. It is central to our understanding of the structure and evolution of proteins. It will play an important role in the interpretation of the sequences produced by the genome projects and therefore in understanding the evolution of .

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