SCOP: a structural classification of proteins database for the investigation of sequences and structures.

  title={SCOP: a structural classification of proteins database for the investigation of sequences and structures.},
  author={Alexey G. Murzin and Steven E. Brenner and Tim J. P. Hubbard and Cyrus Chothia},
  journal={Journal of molecular biology},
  volume={247 4},

Figures and Tables from this paper

SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data.

The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known protein structures. The classification is on hierarchical

SCOP: a structural classification of proteins database

The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures that provide the basis of the ASTRAL sequence libraries that can be used as a source of data to calibrate sequence search algorithms and for the generation of statistics on, or selections of, protein structures.


The structure of a protein can elucidate its function and its evolutionary history, and a discussion of protein evolution from a sequence structure and functional perspective is begun.

SCOP database in 2002: refinements accommodate structural genomics

A new set of features with the aim of standardizing access to the SCOP database, and providing a solid basis to manage the increasing number of experimental structures expected from structural genomics projects are introduced.

SCOP database in 2004: refinements integrate structure and sequence family data

A refinement of the SCOP classification is initiated, which introduces a number of changes mostly at the levels below superfamily, and modernization of the interface capabilities of SCOP allowing more dynamic links with other databases is started.

Classifying a protein in the CATH database of domain structures.

A recently established facility to search the CATH database with the coordinates of a newly determined structure and use automatic sequence and structure comparison methods to assign this new structure to one or more of the domain families within CATH.

ProSeg: a database of local structures of protein segments

The development of a database called ProSeg, which consists of two sub-databases, Segment DB and Cluster DB, which contains tens of thousands of segments that were prepared by dividing the primary sequences of 370 proteins using a sliding L-residue window, is reported.

Protein folds and families: sequence and structure alignments

Dali and HSSP are derived databases organizing protein space in the structurally known regions that provide a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination.

The SUPERFAMILY database in 2004: additions and improvements

The SUPERFAMILY database provides structural assignments to protein sequences and a framework for analysis of the results, which is a library of profile Hidden Markov Models that represent all proteins of known structure based on the SCOP classification of proteins.

Searching ECOD for Homologous Domains by Sequence and Structure

This unit demonstrates how to access ECOD via the Web and how to search the database by sequence or structure and details the distributable data files available for large‐scale bioinformatics users.



Identification and classification of protein fold families.

Analysis of sequence and structure conservation within the larger families shows the globins to be the most highly conserved family and the TIM barrels the most weakly conserved.

The anatomy and taxonomy of protein structure.

Protein structure comparison by alignment of distance matrices.

A novel algorithm (DALI) for optimal pairwise alignment of protein structures that identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions is developed.

Families and the structural relatedness among globular proteins

  • D. YeeK. Dill
  • Biology
    Protein science : a publication of the Protein Society
  • 1993
It is found that protein families are not tightly knit entities, by using an analogy to distributions of Euclidean distances.

Three-dimensional structure of the ATPase fragment of a 70K heat-shock cognate protein

Surprisingly, the nucleotide-binding 'core' of the ATPase fragment has a tertiary structure similar to that of hexokinase, although the remainder of the structures of the two proteins are completely dissimilar, suggesting that both the phosphotransferase mechanism and the substrate-induced conformational change intrinsic to the hexokinases may be used by the 70K heat shock-related proteins.

Structural patterns in globular proteins

A simple diagrammatic representation has been used to show the arrangement of α helices and β sheets in 31 globular proteins, which are classified into four clearly separated classes. The observed

β-Sheet topology and the relatedness of proteins

The topological connectivities of β-pleated sheets in the known protein structures are systematically surveyed for regularly occurring features and suggest that striking topological similarities between different proteins can readily happen by chance.

Structure of proteins: packing of alpha-helices and pleated sheets.

Simple models are presented that describe the rules for almost all the packing that occurs between and among alpha-helices and pleated sheets, which are the major determinants of the three-dimensional structure of proteins.

Principles that determine the structure of proteins.

  • C. Chothia
  • Materials Science, Chemistry
    Annual review of biochemistry
  • 1984
Protein Subunits Buried Between Protein Subunits and Secondary-Structure Surfaces and Residue Composition 564 Chemical Character of Buried and Accessible Surfaces 564 Extent of the Accessible and Buried Sur surfaces 565 Surfaces Buried between protein Subunits 566.