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Structural Bioinformatics, 2nd Edition by Philip E. Bourne, Jenny Gu

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17

PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE

Raghu P. R. Metpally and Boojala V. B. Reddy

INTRODUCTION

The structure of a protein can elucidate its function and its evolutionary history (see Chapters 18, 21 and 23). Extracting this information requires knowledge of the structure and its relationships with other proteins. These in turn require a general knowledge of the folds that proteins adopt and detailed information about the structure of many proteins. Nearly all proteins have structural similarities with other proteins, and in many cases, share a common evolutionary origin. The knowledge of these relationships makes important contributions to structural bioinformatics and other related areas of science. Further, these relationships will play an important role in the interpretation of sequences produced by genome projects. To facilitate understanding and access to the information available for known protein structures, Murzin, Brenner, Hubbard, and Chothia (1995) have constructed a structural classification of proteins (SCOP) database. The SCOP database is based on evolutionary relationships and on the principles that govern their three-dimensional structure. It provides for each entry links to coordinates, images of the structure, interactive viewers, sequence data, and literature references. The database is freely accessible on the World Wide Web (http://scop.mrc-lmb.cam.ac.uk/scop). To understand the rationale behind SCOP, we begin with a discussion of protein evolution ...

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