BaSiLiCo (Binding Site Ligand Contacts) is an online tool to calculate contact strengths for a structural ensemble of binding site–ligand complexes. Choose file with the binding site ensemble to upload and press the 'Calculate' button. Alternatively, provide Pocketome or PDB id.
There are two modes of calculations: ensemble mode and complex mode. In the ensemble mode (i) the ligands are clustered to eliminate chemical redundancy, and (ii) flexibility of the binding site residues is taken into account. This mode is useful to detect most conserved contacts. In the complex mode each ligand–protein complex is treated individually. This mode is useful to highlight differences in the binding pattern of the same ligand.
The following types of files are supported:
- ICM binary files (.icb)
- ICM object files (.ob)
- PDB files (.pdb)
Protein chains must have consistent order and residue numbers. For the ensemble mode objects must be superimposed, preferably by the binding site residues.
Residue tags psite and ligand may be set as in Pocketome files for precise control of the binding site and ligand selections. Otherwise all hetatm molecules are considered as ligands, and protein chains in vicinity of the ligands are considered as a binding site.
If protein chains have SwissProt annotation (ICM command set swiss) and the sequences are present in the file, they will be used for residue codes and mutation labels.
Additional residue selection can be provided to control visualization of the contacts. This optional field is useful for comparison of several aligned proteins. Format of the selection is 'A1/1,2,5,-,-,10|A2/1,2' that means 'select residues 1 and 2 of the chain A1, insert gap of two residues, select residue 10 of the chain A1, select residues 1 and 2 of the chain A2'. In this mode protein molecules must have sequence annotation.