Investigating Interfaces of Macro-Molecular Complexes with Intervor

PROBLEM SPECIFICATION

• detect interface atoms, as well as water molecules squeezed in-between the partners;
• provide a description of the Voronoi interface in terms of patches, surface area, curvature, atomic composition;
• qualify interface atoms and Voronoi tiles as a function of their depth at the interface.

Addditional notes:

• Intervor is based on the Triangulation_3 and Alpha_shape_3 packages of the Computational Geometry Algorithms Library.
• The atomic radii used are the so-called group radii from Chothia and Janin, Nature 256, 1975. Details here.

BIBLIOGRAPHY

Algorithms: Geometric, topological and contact analysis of interfaces in macro-molecular complexes: from the atomic scale to the complex scale using Intervor; INRIA Tech report 5864; F. Cazals, 2006. (Supplemental outdated: see Software paper below.) Structural studies: Revisiting the Voronoi description of Protein-Protein interfaces; F. Cazals, F. Proust, and R. Bahadur, J. Janin; Protein Science, 15 (9), 2006. Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics and composition; Bouvier and R. Grunberg and M. Nilges and F. Cazals; Proteins: Structure, Function, and Bioinformatics, 76(3), 2009. Software Modeling macro-molecular interfaces with Intervor; INRIA Tech report 7069; F. Cazals and S. Loriot, 2009.

INSTRUCTIONS

• 1. Provide a PDB file, with extension .pdb or .PDB
• 2-3. Specify each partner in the complex, as a collection of capital letters identifying the chains. If two or more chains, do not insert blanks in between letters
• 4. Click Discard water molecules if you wish to drop all water crystallographic water molecules
• 5. If you wish to discard only water molecules whose temperature factor is too high, provide its value, in the range 0..100
• 6a-b. Click Filter large Voronoi facets with M if you wish to discard potential large Voronoi facet. If so, provide a value M, in the range 0..100
• 7. By default, Voronoi facets are colored by the interaction type corresponding to the two atoms defining the facet. Clicking the check-box makes the coloring scheme depend upon the shelling order of the facet.

• Calculations are based upon the following classification of atoms and residues.
• This web server requires all occupancy factors to be equal to 1. For a more ellaborate processing, the user should retrieve the binary version of Intervor, learn about the strategies offered in case of factors < 1, and proceed accordingly.
• In case of alternates, the first occurance is the one selected.

RUNNING A CALCULATION

DOWNLOADING THE EXECUTABLE

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.

See the VMD page for the plugin installation instructions.

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