SCOP: Structural Classification of Proteins

Welcome to SCOP: Structural Classification of Proteins. 1.65 release (December 2003).
20619 PDB Entries. 1 Literature Reference. 54745 Domains (excluding nucleic acids and theoretical models). Folds, superfamilies, and families statistics here. New folds superfamilies families. List of obsolete entries and their replacements.

Authors. Alexey G. Murzin, Loredana Lo Conte, Antonina Andreeva, Dave Howorth, Bartlett G. Ailey, Steven E. Brenner, Tim J. P. Hubbard, and Cyrus Chothia. 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. [PDF]
Major changes (stable identifiers, parseable files, extended searching and linking options, reclassified entries history) are described in: Lo Conte L., Brenner S. E., Hubbard T.J.P., Chothia C., Murzin A. (2002). SCOP database in 2002: refinements accommodate structural genomics. Nucl. Acid Res. 30(1), 264-267. [PDF].
Andreeva A., Howorth D., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A.G. (2004). SCOP database in 2004: refinements integrate structure and sequence family data. Nucl. Acid Res. 32:D226-D229.

Access methods

Enter SCOP at the top of the hierarchy
Keyword search of SCOP entries
SCOP parseable files
All SCOP releases and reclassified entry history
SCOP domain sequences and pdb-style coordinate files (ASTRAL)
Hidden Markov Model library for SCOP superfamilies (SUPERFAMILY)
Online resources of potential interest to SCOP users

SCOP mirrors around the world may speed your access.

News

SCOP has been updated to include all PDB entries released up to 1 August 2003. See folds, superfamilies, and families statistics.
Several parts of the SCOP classification have been restructured, especially in this release and in the previous one. You can brouse the subset of the classification affected by these changes in a SCOP-view form for modifications occurred between 1.63 and 1.65, as well as in previous releases. Changes appear as comments associated to domain entries, with links to the revised classification. You can use the SCOP navigation buttons to move up in the hierarchy and to expand or collapse entries. A list of obsolete entries and their replacements, starting from release 1.57, is also available online.
SCOP identifiers now appear explicitly in the web pages (in square brackets).
Links from a SCOP domain to the corresponding SWISSPROT and EC entries have been added (see the icon). Thanks to Sameer Velankar and Phil McNeil from the EBI-MSD group and to Virginie Mittard from the EBI sequence database group for providing the most up-to-date map between PDB chains and SWISSPROT, EC identifiers.
Links to the analysis of Non Canonical Interactions (NCI) for SCOP domains are also available via the icon. See non canonical interactions for d2hft_1 [sunid=21951] for example.
It is now possible to use SSM to search the up-to-date PDB archive using a SCOP domain entry (via the icon) or to search SCOP using a PDB not yet classified in SCOP.
You can also search several text fields in a PDB file and get links to the corresponding SCOP entries using the MSDlite search engine as one of the options for search engine.
Please read the release notes. They have been updated and now contain more detailed explanations and examples of all new and not so new SCOP features.
New features can be added to SCOP in between releases. Stay tuned.
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

Structural similarity search of SCOP using SSM
Combinatorial Extension (CE) method for structural comparison
PALI pairwise and multiple alignments of SCOP families
SUPFAM structure/sequence relationships
Stuctural similarity search of SCOP using 3dSearch
Stuctural alignment of SCOP sequences (database + server)
PINTS - Patterns In Non-homologous Tertiary Structures
Sequence similarity search of SCOP using FPS
CATH structural classification
Dali structural comparison and FSSP structural classification
PDB at a Glance
3Dee Protein Domain Definitions
Protein Data Bank (PDB)
Macromolecular Structure Database (EBI)
Nucleic Acid Database (NDB)
Swiss-Model
Macromolecular Motions Database
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

December 2003