About CSM-Potential

CSM-Potential is a valuable resource for the study areas of a protein surface that are likely to mediate protein-protein and protein-ligand interactions.

Running predictions

CSM-Potential offers two types of predictions via the Run menu:

  • Identification of PPI Sites
  • Biological Ligand Classification
In both cases, users are only required to provide a protein structure of interest, by either uploading it in PDB format (1) or providing the PDB accession code (2).
Input PPI binding site identification

Users may select specific monomers of the input structure via the chain identifiers field (3). If empty all chains will be considered

Users are required to provide a protein structure by uploading a file in PDB format or typing a PDB four letter accession code (2).

If provided (4), an email will be sent to the user after the submission is processed.

A button for an example results page is available at the bottom of the form (5)

When running Biological Ligand Classification, after submitting the protein structure, one is required to select the pocket (6) region to be used during classification.

Pocket selection for biological ligand classification
Results - Identification of PPI Sites
Results for PPI binding site identification
  • Results are summarised in relation to the sequence of amino acids present in each chain of the submitted protein structure (7), and also as an interactive 3D viewer (8) where scores for each residue are mapped onto the input structure.
  • A set of controllers and action buttons are available for customising the 3D viewer (9).
Results - Biological Ligand Classification
Table in results page for systematic evaluation of a PPI interface
  • Results are summarised in table format with scores for each of the 7 ligands (10). For each ligand, a "Details" is available where users can visualise its depition and also relevant information about physicochemical properties.
  • An interactive 3D viewer is also available where the pocket region used during the classification is highlighted (11).
  • A set of controllers and action buttons are available for customising the 3D viewer (12).
Contact us

In case you experience any troube using CSM-Potential or if you have any suggestions or comments, please do not hesitate in cantacting us either via email or via our Group website.

If your are contacting regarding a job submission, please include details such as input information and the job identifier