Main page

About CSM-lig

CSM-lig is a machine-learning method to predict affinities of small-molecules to proteins, which relies on distance/pharmacophore patterns encoded as graph-based signatures.

A user-friendly and freely accessible web interface was developed and allows users to submit either a single PDB structure of the protein-small molecule complex, or a compressed file with multiple structures, which could include different poses of the same complex, different ligands or multiple different proteins.

Submission page

How to run a prediction

To run a prediction:

• Click on "Predict" (1) to open the submission page.


• Provide either:
  • A single PDB file and the small-molecule information (HET ID and SMILES string) (2) or
  • As input files, a compressed file with PDBs (.zip) and a tab-separated file with the molecule information (HET ID and SMILES string for each uploaded PDB)(3).

Users are advised to use Canonical SMILES. Syntax non-compliant molecules or PDB files will be ignored.

Parsing Considerations

* Water molecules present in the uploaded PDB files are removed prior to calculation.
* Cofactors, metals and ions are also removed from the structure and are not considered in the structural signature calculations.

Results page

Results

For a single molecule prediction, your results can be displayed as follows:

• The affinity prediction will be shown in (1).


• A depiction of the small-molecule will be shown in (2). Make sure the depiction is what you are expecting for your molecule.


• A list of molecule properties will be calculated and shown in (3).


• An interactive molecular visualization of the uploaded complex will be shown in (4).


• Users have the option to download a Pymol session file for visualizing the ligand interactions in (5).


• There is also an option of calculating the phamacokinetic and toxicity properties of the ligand using the pkCSM server (6).

Results for multiple molecules will be shown in a tabular format, whithout molecule depiction, which can be downloaded as a tab-separated file.

Contact page

Getting in touch

In case you experience any trouble using CSM-lig or have any suggestions or comments, please do not hesitate in contacting us either via e-mail or through the online form.