CMMC

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A server for calculating contact maps of X-ray, NMR and predicted structures

Introduction to COCOMAPS


COCOMAPS (bioCOmplexes COntact MAPS) is a web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of intermolecular contact maps.

The user only needs to: i) download input files directly from the wwPDB or upload her/his own PDB formatted files and ii) specify the chain identifiers for the molecules involved in the interaction to be analysed. Please note that more chains can be selected for each interacting partner.

COCOMAPS output includes three different contact maps, as well as tables reporting detailed information about the interacting residues (defined on the basis of a cut-off distance that can be customized by the user), the residues at the interfaces (defined on the basis of the buried surface upon complex formation), and the inter-molecular H-bonds. A 3D visualization of the complex in JMol is also provided online and a ready-to-run Pymol script, which generates a visualization of the interface, is downloadable.

COCOMAPS is freely available to the scientific community as a complementary tool in the study of interfaces. It can straightforwardly be applied to the analysis, visualization and comparison of both experimental and predicted 3D structures of biological complexes.

To analyse and rank multiple docking solutions go to CONSRank

Data Entry

OPTION 1: Enter a single PDB code and the chain identifiers for the interacting molecules.

(e.g 2ZA4)
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(e.g A or A B)
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(e.g C or C D)
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OPTION 2: Upolad coordinates of one or two PDB files and enter the chain identifiers of the interacting molecules.

1 file
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(e.g A or A B)
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(e.g C or C D)
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2 files
Cut-Off Help Page

Threshold distance to select interacting residues in Å (default value:8 Å)
Advanced Options (Optional)

(No white-space)
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