SCOP2 prototype: a new approach to protein structure mining.

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.