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PPIC: Computes the interface protein-protein or protein-ligand.

References:

V. Ozeel, A. Perrier, A. Vanet, M. Petitjean
The Symmetric Difference Distance: A New Way to Evaluate the Evolution of Interfaces
along Molecular Dynamics Trajectories; Application to Influenza Hemagglutinin.
Symmetry, 2019, 11[5], 662. DOI 10.3390/sym11050662

P. Laville, J. Martin, G. Launay, L. Regad, A.-C. Camproux, S. de Vries, M. Petitjean
A non-parametric method to compute protein-protein and protein-ligands interfaces.
Application to HIV-2 protease-inhibitors complexes.
BIORXIV/2018/498923. DOI 10.1101/498923
http://biorxiv.org/cgi/content/short/498923v1

N. Cerisier, L. Regad, D. Triki, A.-C. Camproux, M. Petitjean,
Cavity versus ligand shape descriptors: Application to urokinase binding pockets.
J. Comput. Biol., 2017, 24[11], 1134-1137. DOI 10.1089/cmb.2017.0061

Author email: petitjean.chiral@gmail.com

PPIC reads the cartesian coordinates of two structures in PDB format,
then returns the two lists of atoms at their interface. 
The structures should be concatenated into a single PDB file prior execution.
This input file can contain any number of PDB structures.


Input data and parameters:
-------------------------

INPUT  PDB FILE NAME:
     Name of the input file containing both structures.
     Only HEADER, ATOM, ENDMDL and END records are recognized
     (other records are read as comments)..
     Each structure must begin by a HEADER line and must end either by END or by ENDMDL.


OUTPUT PDB FILE NAME:
     Name of the output file containing both lists of atoms at the interface.

IPDB1: sequential position number of structure 1 in the input PDB file

IPDB2: sequential position number of structure 2 in the input PDB file

METHOD: enter 1 or 2 or 3
        If METHOD=1 (default), the method of Ceriser et al. applies.
           An atom of protein 1 is in the interface if
           it is the closest neighbour of an atom of protein 2
        If method=2, the Voronoi method applies.
           An atom of protein 1 is in the interface if
           its Voronoi cell shares a face with the Voronoi cell of an atom of protein 2.
        If method=3, the cut-off distance criteria applies.
           An atom of protein 1 is in the interface if
           its distance to an atom of protein 2 is less or equal than to
           the cut-off distance defined by PARAM

PARAM: cut-off distance (default is 0).
       This parameter is required only when METHOD=3.


Output results:
--------------

In the output PDB file, there are two lists of atoms.
The first  one is a subset of the atoms of the first  PDB structure (IPDB1).
The second one is a subset of the atoms of the second PDB structure (IPDB2).
These two lists constitute the interface protein-protein or protein-ligand.

NEAREST NEIGHBOURS LIST 1:
List of the nearest neighbours for the interface part of the first  PDB structure (IPDB1).

NEAREST NEIGHBOURS LIST 2:
List of the nearest neighbours for the interface part of the second PDB structure (IPDB2).

RNN analysis:
A pairwise correspondence between the atoms of the two lists above is output on the screen.
Not all atoms of these two lists are cited in the pairwise correspondence.


Remarks:
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The paired atoms computed by the RNN analysis may be assumed to be part of the
interaction site, while there is no guarantee about the validity of this assumption.

The number of atoms is currently limited to 50000 for each input PDB structure.
The source has to be recompiled to read larger ones.


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