[3dem] PDBePISA assembly,
summary and XML data files available from the
Protein Data Bank in Europe
Gerard DVD Kleywegt
gerard at xray.bmc.uu.se
Wed Aug 18 13:31:18 PDT 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.
Please point your browser to:
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:
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
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 J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard at ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_admin at ebi.ac.uk
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