Networks of Protein Interfaces
What are you getting?
How to use it?
Our server helps you with the exploration of macromolecular interfaces.
We run the given PDB through PISA (
P
rotein
I
nterfaces,
S
urfaces,
A
ssemblies) program (a part of CCP4 suite) to obtain the interfaces data in XML format.
Next, we embed this information into a network compatible with Cytoscape (popular network viewer).
We provide a fully constructed Cytoscape session with predefined configuration of CyToStruct plug-in that allows the user to view the interfaces in her favorite molecular viewer.
For a given PDB file the server responds with a single .zip archive containing:
'
protein.pdb
' - the original PDB.
'
network.txt
' - this is the network data for Cytoscape and CyToStruct.
'
network.sif
' - a copy of the network we are using in the session file
'
name.cys
' - predefined session for Cytoscape, where name is the name of your protein
'
pisa.yaml
' - a copy of CyToStruct configuration set in the session file
'
README.txt
' - help file.
Related work:
Original PISA paper:
E. Krissinel and K. Henrick (2007).
'Inference of macromolecular assemblies from crystalline state.'
. J. Mol. Biol.
372
, 774--797.
PDBePISA server: Interactive tool
PDBePISA
COCOMAPS server: A server for calculating contact maps
COCOMAPS
