[X-plor] PDBePISA assembly, summary and XML data files available from the Protein Data Bank in Europe

Gerard DVD Kleywegt via x-plor%40net.bio.net (by gerard from xray.bmc.uu.se)
Wed Aug 18 15:30:35 EST 2010


The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to 
announce the availability of PISA assembly files, summaries and associated XML 
descriptors for all relevant entries in the Protein Data Bank (PDB) archive 
for download and in-house analysis.

PDBePISA (http://pdbe.org/pisa/) is an advanced interactive tool for the 
prediction of probable quaternary structures (assemblies), analysis of 
macromolecular interfaces and surfaces, database searches for similar 
interfaces and assemblies, and retrieval of results based on various search 
criteria. PDBePISA also allows the upload of your own structure in PDB or 
mmCIF format for interface analysis or quaternary structure prediction.

PDBePISA-predicted stable assembly files in PDB format are now available for 
download from the PDBe FTP area for all structures determined by diffraction 
methods. In addition, interface parameters (interface contacts, symmetry 
operators, hydrogen and disulphide bonds, salt bridges etc.) and assembly 
parameters (overall and buried surface areas, dissociation energies, contact 
interface characteristics) are available for every entry in XML format for 
further analysis. A summary index file is also provided in the FTP area 
containing a one-line summary for every stable assembly predicted by PDBePISA. 
This file provides an at-a-glance summary of the salient features of every 
stable assembly predicted by the program. This area is updated every Wednesday 
to coincide with the public update of the PDB archive.

DATA ACCESS
-----------

Please point your browser to:

      ftp://ftp.ebi.ac.uk/pub/databases/msd/pisa/

The file ftp://ftp.ebi.ac.uk/pub/databases/msd/pisa/index.txt contains the 
one-line summary for each assembly in column delimited format.

Individual entry data may be found in a path like this:

      ftp://ftp.ebi.ac.uk/pub/databases/msd/pisa/data/xx/1xxx/

where 'xx' are the second and third characters of the PDB id code and 1xxx is 
the actual PDB id code. For example, information for PDB entry 1cbr may be 
found under

      ftp://ftp.ebi.ac.uk/pub/databases/msd/pisa/data/cb/1cbr/

The files in this directory will have names like

- 1xxx.pdb.gz or 1xxx_n.pdb.gz for the assembly files (where 'n' is the 
assembly number when PDBePISA predicts multiple assemblies).

- 1xxx_assembly.xml.gz : The assembly description in XML.

- 1xxx_interface.xml.gz: The interface description in XML.

As always, we welcome comments and suggestions on new features (preferably 
using the big, fat "FEEDBACK" button on the PDBe web pages).

--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin from ebi.ac.uk



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