New features in SCOP and ASTRAL (release 1.55)

John-Marc Chandonia JMChandonia at lbl.gov
Thu Jul 19 17:47:43 EST 2001


New features in SCOP and ASTRAL

The SCOP: Structural Classification of Proteins database is a
comprehensive ordering of all proteins of known structures 
according to their structural and evolutionary relationships.

The ASTRAL compendium provides databases and tools useful for
analyzing protein structures and their sequences.  It is partially
derived from, and augments SCOP in several ways, in particular by 
providing sequence information about SCOP domains, and a mapping 
between SEQRES and ATOM fields in PDB files.

The SCOP release 1.55 is now available at:
    http://scop.mrc-lmb.cam.ac.uk/scop/

and, shortly, at the SCOP mirror sites.

The associated ASTRAL release 1.55 is available at:
    http://astral.stanford.edu/

Although this release is superficially similar to previous ones, 
there are several innovations and new features that may affect 
the way you use these databases.

- As announced in September 2000, all SCOP pages for release 1.55 have
been renamed. If you still link to SCOP using a page name, despite
this having been deprecated since 1994, this time all your links will
be broken.

- SCOP 1.55 is based on a new set of identifiers which are expected to
be stable across releases. There is a new set of parseable files, based
on the new identifiers. The standard ASTRAL SCOP domain sequences have
been modified to reflect the new SCOP identifiers, and the FASTA header
format is slightly different.
- A new set of genetic domain sequences is available at the ASTRAL web
site, together with a new rapid access format file (RAF) with a manually
curated mapping between SEQRES and ATOM fields for all PDB chains in 
SCOP class 1-7. This latter provides users with the official definition 
of a domain in terms of: a) SEQRES sequence; b) ATOM sequence; c) mapping
between the two sequences; and d) the original PDB residue identifiers
from the ATOM field, which uniquely define the domain in terms of PDB
coordinates.

A great effort has been made in removing all known errors and providing
a clean and standardized data set. We would like to take the opportunity
to encourage you to use these reference data in your research work. This
will make comparison, linking, and integration of SCOP-based results a  
trivial task. The purpose is to develop a common language that we can use
without ambiguities when talking about a SCOP domain and its classification.

Please read the SCOP release notes:

       http://scop.mrc-lmb.cam.ac.uk/scop/release-notes-1.55.html

and the ASTRAL release notes:

    http://astral.stanford.edu/scopseq-1.55/release-notes-1.55.txt

for more detailed information, and don't hesitate to get in touch with us,
should you have any further questions.

Loredana Lo Conte                       John-Marc Chandonia
for the scop authors                    for the ASTRAL authors
scop at mrc-lmb.cam.ac.uk                  astral at compbio.berkeley.edu




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