SCOP2 prototype: a new approach to protein structure mining

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.

Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis

“…Superposition and r.m.s.d. of the structures were calculated using LSQMAN (32), and folding motifs were classified in the SCOP2 database (33). All structure figures were prepared using PyMOL (34) or UCSF Chimera (35).…”

The Protein Data Bank archive as an open data resource

“…More than 400 million coordinate sets were downloaded in 2013 from the wwPDB partner sites. Both the utility and the uniformity of PDB data have enabled the development of other databases and datarelated resources, including resources for drug discovery (for a review see [32]); resources focused on small molecules and ligands such as ChEMBL [33], DrugBank [34], BindingDB [35], BindingMOAD [36], and PDBBind [37]; protein structure classification and annotation resources, such as CATH [38,39], SCOP [40][41][42], and PDBsum [43,44]; and focused, specialty annotation resources such as Protein Data Bank of Transmembrane Proteins (PDBTM) [45], ArchDB for functional loops in structures [46], and 3did for protein-protein interaction surfaces [47]. These resources are frequently compiled in the annual Database Issue of Nucleic Acids Research.…”

Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics

“…This is indeed observed in nature as well as in models. Based on the database of structural classification of proteins [40,41], the number of folds (corresponding to the structures) is much smaller than the number of domains (corresponding to sequences), which demonstrates the mapping from multiple sequences to one structure. With a model with two kinds of monomers, the sequence space could be characterized by the concept of voronoi cells in solid physics [42].…”