scop news

• Using a new updating procedure, we have partly classified PDB releases between January 2005 and April 2007. Pre-classification of new structures was computed and imported into a relational database.
• Manual curation of the representative structures of a cluster of identical sequences was carried out incrementally by Family and Superfamily. Priority was given to representatives of new sequence families, in particular those targeted by structural genomics initiatives. This allowed a rapid accumulation of new SCOP families, superfamilies and folds. These curated structures were merged into the SCOP hierarchy.
• Related structures with identical and nearly identical sequences to these representatives in the relational database and to previously classified structures in SCOP 1.71 were added automatically.
• This release is similar in appearance to the previous release, so the generic release notes from that release still apply. Please read the notes; they contain more detailed explanations and examples of SCOP features.

• SCOP has been updated to include all PDB entries released up to 18 January 2005. See folds, superfamilies, and families statistics.
• This release, corresponding to the PDB snapshot at the beginning of 2005, is the last one that classifies all PDB structures released before a certain date. The process of classification of new entries has been changed. For more information please visit pre-SCOP - a preview of the next release.
• This release is similar in appearance to the previous release, so the generic release notes from that release still apply. Please read the notes; they contain more detailed explanations and examples of SCOP features.

• SCOP has been updated to include all PDB entries released up to 1 October 2004. See folds, superfamilies, and families statistics.
• The process of SCOP production is gradually being changed and has resulted in some internal and external database information being incorporated in new names and comments. This information is primarily intended for use in the ongoing SCOP redevelopment but it has been displayed on the web pages as it may be of some help to users.
• This release is similar in appearance to the previous release, so the generic release notes from that release still apply. Please read the notes; they contain more detailed explanations and examples of SCOP features.

• SCOP has been updated to include all PDB entries released up to 15 May 2004. See folds, superfamilies, and families statistics.
• Please note that SCOP unique identifier (sunid) values have exceeded 100,000 in this release, so some sunids are now 6 digits long. You may need to update any code that assumes these are exactly 5 digits.
• 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.

• 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.

• SCOP has been updated to include all PDB entries released up to 1 March 2003. See folds, superfamilies, and families statistics.
• Several parts of the SCOP classification have been restructured in this release. A summary of major changes can be found here, together with a detailed history of rearrangements, lists of new folds, new superfamilies, new families, and obsolete entries since 1.55.
• Mirror sites with and without local PDB files should behave in the same way from the user point of view.
• Most of the options of the old PDB viewer and some external links previously associated with different icons for the same SCOP entry are now available via the icon. There are also some new options, such as a structural similarity search of the SCOP database using SSM. If you think your work is of interest for our users, please get in touch with us.
• There is a new parseable file, dir.com.scop.txt, including all comments in SCOP.
• It is now possible to add new features to SCOP in between releases. Stay tuned.

• SCOP has been updated to include all PDB entries until 1 September 2002. See folds, superfamilies, and families statistics.
• A full history, comprising a list of new folds, new superfamilies, new families, as well as obsolete entries since 1.55, is available online. Equivalent data for the previous release can be retrieved using the search engine: see folds, superfamilies, and families that first appeared in SCOP 1.59.
• Protein structures known to come from structural genomics projects can be also be retrieved using the keyword option of the search engine.
• Entries in the dir.des.scop.txt parseable file are now ordered according to the SCOP hierarchy.
• Thanks to Raphaël Leplae for help with chime.

• SCOP has been updated to include all PDB entries until 1 March 2002. See folds, superfamilies, and families statistics.
• A full history, comprising a list of new folds, new superfamilies, new families, as well as obsolete entries since 1.55, is now available online.
• Protein structures known to come from structural genomics projects can be retrieved using the keyword option of the search engine.

• SCOP has been updated to include all entries until 1 Oct 2001. See folds, superfamilies, and families statistics.
• Previous SCOP releases are available online at the MRC site.
• The new set of identifiers introduced in SCOP 1.55 is stable. An identifier always refers to the same entry. If the entry was modified, the old identifier becomes obsolete and the user is redirected to the corresponding new entry in the current release. Follow the fate of a.4.4, for example. An easy-to-parse history will be made available soon.
• For each SCOP domain in class 1-7, there is an icon () which provides a set of links to information related to that domain in Pfam, SUPERFAMILY, PARTS LIST, and, in case there is a corresponding entry, in PRESAGE and SCOR.
• Thanks to Raphaël Leplae (lp1@sanger.ac.uk), an improved version of RmscopII is now available for UNIX/Linux, MAC and MS Windows platforms.

For each SCOP domain in class 1-7, there is a new icon () which provides a set of links to information related to that domain in Pfam, SUPERFAMILY, PARTS LIST, and, in case there is one or more sequences predicted to have that fold, to PRESAGE.

• SCOP has been updated to include all PDB entries until 1 Mar 2001. See folds, superfamilies, and families statistics.
• This release is based on a new set of identifiers which are expected to be stable across SCOP releases.
• There is a new set of parseable files, based on the new identifiers.
• ASTRAL SCOP domain sequences have been modified to reflect the new identifiers.
• A new set of genetic domain sequences and a new rapid access format file with a manually curated mapping between SEQRES and ATOM fields for all PDB chains in class 1-7 are available at the ASTRAL web site.
• An effort has been made to normalize species in SCOP. Thanks to Sameer Velankar (sameer@ebi.ac.uk), Virginie Mittard (virginie@ebi.ac.uk), and Phil Mcneil (mcneil@ebi.ac.uk) for providing the most up-to-date correspondence between PDB and SwissProt identifiers.
• Thanks to Shyam Prabhakar (shyam@gnomic.berkeley.edu) for providing a more general version of rmscop for linux/unix users.

• 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.

• SCOP has been updated to include all PDB entries until 29 Feb 2000. See folds, superfamilies, and families statistics.
• From this release (i.e. from year 2000) SCOP domain identifiers are expected to be stable and change only if the domain definition changes significantly. Changes will be recorded and a history will be provided. Read more about reliably linking to SCOP.
• The keyword search has been modified.
• Viewing structures with RasMol.

• SCOP has been updated to include all PDB entries until 1 Nov 1999. See folds, superfamilies, and families statistics.
• Sequences corresponding to SCOP domains, filtered according to different criteria, can be obtained from the ASTRAL domain sequences site.
  Reference: Brenner S. E., Koehl P., Levitt M. (2000). The ASTRAL compendium for sequence and structure analysis. Nucleic Acid Research, 28:254-256.
• A PDB sequence similarity search using a library of intermediate homologs is now available (PDB-ISL).
  Reference: Teichmann, S. A., Chothia, C., Church, G. M. and Park, J.
  Fast Assignment of Protein Structures to Sequences using the Intermediate Sequense Library PDB-ISL, Bioinformatics, 16:117-124.
• The BLAST sequence similarity search for SCOP entries is not available at the moment.