Structural Classification of Proteins

Welcome to SCOP: Structural Classification of Proteins. 1.53 release.
11410 PDB Entries (1 Jul 2000). 40 Literature References. 26219 Domains (excluding nucleic acids and theoretical models). Folds, superfamilies, and families statistics here.

Authors. Alexey G. Murzin, Loredana Lo Conte, Bartlett G. Ailey, Steven E. Brenner, Tim J. P. Hubbard, and Cyrus Chothia.

MRC Laboratory of Molecular Biology and Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH, England. scop@mrc-lmb.cam.ac.uk

Reference: Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.

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Access methods

• Enter SCOP at the top of the hierarchy
• Keyword search of SCOP entries
• PDB entry viewer
• SCOP sequence libraries and parseable files
• All SCOP releases and reclassified entry history
• SCOP domain sequences (ASTRAL)

• Hidden Markov Model library for SCOP superfamilies (SUPERFAMILY)
• Intermediate Sequence Library (PDB-ISL)
• Online resources of potential interest to SCOP users

News

• SCOP has been updated to include all PDB entries until 1 Jul 2000. See folds, superfamilies, and families statistics.
• A Hidden Markov Model library based on SCOP 1.50 superfamilies is now available (SUPERFAMILY).
  Preliminary work is described in: Gough, J.G.,Chothia C., Karplus K., Barrett C., Hughey R. (2000). Optimal Hidden Markov Models for all sequences of known structure. Currents in Computational Molecular Biology, 124-125. Miyano S., Shamir R., Toshihisa T. eds. Universal Acadamy Press Inc. Tokyo, Japan.
  A full description of SUPERFAMILY (Gough et al.) is in preparation.

• Previous releases' news.

Synopsis

Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.

A more detailed description of the database is available. Help on using the database may be obtained on any screen by pressing the question mark button.

Online resources of potential interest to scop users

• Sequence similarity search of SCOP using FPS.
• Stucture similarity search of SCOP using 3dSearch or TOP.
• Stuctural alignment of SCOP sequences (database + server).
• Macromolecular Motions Database.

• Protein Data Bank (PDB).
• Nucleic Acid Database (NDB).
• CATH structural classification.
• Dali structure comparison and FSSP structure classification.
• Combinatorial Extension (CE) method for structural comparison.
• PDB at a Glance.
• 3Dee Protein Domain Definitions.
• Swiss-Model.

• The PRESAGE Database for Structural Genomics.
• Genome Census.
• Function assignment and metabolic models.

• Licensing information for commercial users (MRC site).
• Glossary of terms used in the fold classification.
• References related to fold classification methods and fold definitions.