Abstract
We present a prototype of a new structural classification of proteins, SCOP2 (http://scop2.mrc-lmb.cam.ac.uk/), that we have developed recently. SCOP2 is a successor to the Structural Classification of Proteins (SCOP, http://scop.mrc-lmb.cam.ac.uk/scop/) database. Similarly to SCOP, the main focus of SCOP2 is to organize structurally characterized proteins according to their structural and evolutionary relationships. SCOP2 was designed to provide a more advanced framework for protein structure annotation and classification. It defines a new approach to the classification of proteins that is essentially different from SCOP, but retains its best features. The SCOP2 classification is described in terms of a directed acyclic graph in which nodes form a complex network of many-to-many relationships and are represented by a region of protein structure and sequence. The new classification project is expected to ensure new advances in the field and open new areas of research.
Highlights
Two decades have passed since the Structural Classification of Proteins (SCOP) database was created at the Medical Research Council (MRC) Laboratory of Molecular Biology and Centre of Protein Engineering in Cambridge [1]
The SCOP project has brought together a number of previous studies on the principles of protein structure and evolution [2,3,4,5,6,7,8,9]
SCOP2 retains the best features of the old SCOP database but it differs in several key aspects and provides new data not available in the old resource
Summary
Two decades have passed since the Structural Classification of Proteins (SCOP) database was created at the MRC Laboratory of Molecular Biology and Centre of Protein Engineering in Cambridge [1]. The notion of protein evolution, embodied in SCOP, allowed the discrete grouping of proteins based on their structural similarity and on their probable evolutionary origin. In accordance with the degree of evolutionary divergence and, respectively, structural (dis)similarity, SCOP organized protein domains into families and superfamilies.
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