Investigating Macro-Molecular Interfaces with Intervor

Protein - Protein; Protein - Nucleic Acid; Protein - Drug


PROBLEM SPECIFICATION

Given a macro-molecular complex featuring two partners and possibly water molecules, an interface between these partners is defined as a collection of Voronoi faces separating them; equivalently, each facet identifies two interface atoms. See the bibliography below for a precise description of the interface. The goal of Intervor is to:

Addditional notes:


BIBLIOGRAPHY

Algorithms

Structural studies

Software

  • [CL10] Modeling macro-molecular interfaces with Intervor; S. Loriot and F. Cazals; Bioinformatics 26 (7); 2010.
    Also available as INRIA Tech Report .

Misc

  • [TTCG99] The packing density in proteins: standard radii and volumes. J. Tsai, R. Taylor, C. Chothia, and M. Gerstein. Journal of Molecular Biology, 290(1):253-266, 1999.

INSTRUCTIONS

Important notes:

RUNNING A CALCULATION

Please send comments / error reports / wishes to abs-software@lists-sop.inria.fr
If you use Intervor for a publication, please notify us at abs-software@lists-sop.inria.fr

1.Your data file:
2. First partner:
3. Second partner:
4. Discard strutural water
5. Filter water molecules. Max temperature factor:
6a. Filter large Voronoi facets with M
6b. M (default) value:
7. Color interface facets by shelling order

Note: upon termination, your browser will display a link to the the tgz bundle containing the results.

Your mail (optional):



DOWNLOADING THE EXECUTABLE

Important notes:
First name:
Last name:
Institution:
E-mail address:
Download page here (authentification requested)



Using Intervor within VMD

The plugin Intervor-vmd-plugin allows one to run a calculation and see the result in VMD.

As an alternative, one can (i) run a calculation from the command-line using the binary executable, (ii) generate a vmd file using the vor2vmd.pl perl script available within the Intervor-vmd-plugin bundle, and (iii) load this file within VMD using the Fast load plugin. The bundle provided upon running a calculation from this web site contains the vmd file to be loaded with Fast load.

Help to install the plugins:



Using Intervor within PyMOL

The plugin Intervor-pymol-plugin allows one to run a calculation and see the result in VMD. The bundle provided upon running a calculation from this web site contains the pymol file to be loaded within Pymol.


Gallery

Complex 1vfb: Protein - Protein

(a)Side view of complex

(b)Interface and interface water molecules

Complex 1KX5: Protein - Nucleic Acid

(a)Complex DNA - histones, with structural water at the interface

(b)Interface patches

Complex 2ifb: Protein - Drug

Drug trapped in binding site


Contact: abs-software@lists-sop.inria.fr

Web: F. Cazals