Authors: Antonina Andreeva, Dave Howorth, and Alexey G. Murzin

Disclaimer

This 'snapshot' of the SCOP developmental version is provided 'as is' for the benefit of users interested in the classification of new structures since the 'official' SCOP 1.73 release. Subject to changes without notice. Use at your own risk.


Method

Using a new updating procedure, we have partly classified PDB releases between January 2005 and October 2008*. 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 ( statistics). 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 1.73 were added automatically.

Content

It contains all PDB structures released before January 2005 (as in the 1.71 release) plus a part of the PDB releases between January 2005 and October 2008. These include most 'new family' structures from 'official' Structural Genomics centres registered in the PSI TargetDB.

Existing entries retain the same stable sunids as in the 1.73 release. New nodes are assigned six-digit identifiers starting with 999999 and counting down. These are chosen to be clearly different to the 1.73 sunids and they are unique for this particular version only.

The curated relationships between SCOP and Pfam families are added as comments (usually at Family level). Similarly, many comments at Species level include UniProt accession codes and - for the curated structures - domain boundaries assigned to the corresponding UniProt sequences. Species nodes also include NCBI taxids.

pre-SCOP also lists the provisional classifications derived from automatic sequence comparisons. These are displayed on family pages for those PDB chains assigned to the family.

Navigation

The pre-SCOP hierarchy can browsed in a similar way to SCOP. Note that the external links are different, and some functionalities of SCOP, such as a molecular viewer, are not available.

Keyword search

Pre-SCOP can be searched with any words that appear on its pages, including PDB identifiers, SCOP 1.73 sunid, and - for most recent entries - UniProt and Pfam accession codes. Append a '*' character when searching for external accession codes, just as for free text.

Updates

The developmental version is subject to test and various checks before its conversion into the next SCOP release. There almost certainly will be some changes of the present classifications. In the case of major changes, depending on the users' expressed interest, pre-SCOP can be updated before the next scop release takes place.

pre-SCOP parseable files analogous to the corresponding SCOP parseable files are available. There are no sid and sccs assigned for the new nodes. scop.species.attributes.2008-12-15 is a new file that contains a tabulation of the sunid of SCOP species nodes and their corresponding NCBI taxid.

Send your comments and suggestions to agm@mrc-lmb.cam.ac.uk