Interface analysis servers

The purpose of this article is to list and evaluate servers that analyze interfaces within molecular models, such as protein-protein, DNA-protein, RNA-protein, and ligand-protein interfaces.

COCOMAPSCOCOMAPS

COCOMAPS analyzes and visualizes interfaces in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes). The interface(s) to analyze are specified with the chain identifiers in the PDB file. 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), the inter-molecular H-bonds, the buried area, and the interface areas (both as Ų and percentages).

CommentsComments

• The buried and interfacial areas are not affected by the distance specified when submitting the job.

• Note that the Table of minimum distances lists only the minimum interatomic distance for each pair of residues, not all interatomic distances. The list of all can be obtained by clicking Open table under Distance table. However it is not filterable or sortable at the time of this writing (March, 2012).

PDBsumPDBsum

Every PDB structure page in Proteopedia links to PDBsum under the structure window where it says 'Resources'. The PDBsum page for every structure includes pre-calculated data summarizing protein-protein interactions and buried surface area, protein-nucleic acid, ligand interactions and available clefts, among other data. The data are accessible via links at the top where you will see 'Prot-prot', 'Ligands', 'Clefts,' etc. depending upon what is available. Note that the protein-nucleic acid interactions, if present, will be found on the page that is accessible via the 'DNA/RNA' link -- there will be a link for the NUCPLOT data.
It is also possible to upload your own data and get a similar report generated that contains this information.