[POCKETOME]
 

Find similar sites

This form can be used to search for Pocketome entries that are similar to the given binding site. To perform the search, choose file with the protein structure to upload and press the 'Find similar' button.

File
Selection

The following types of files are currently supported:

  • PDB files (.pdb)
  • ICM binary files (.icb)
  • ICM object files (.ob)

Protein chains must have consistent order and residue numbers across the objects. At least five non-glycine residues must be present in the binding site selection.

For protein–ligand complexes, 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. In this mode residues will be weighted by BaSiLiCo.

Alternatively, residue selection can be provided separately. This is useful in case of an apo structure. In this mode residues will have equal weigth. Syntax of the Selection field is a subset of ICM selection patterns. Namely, these elements are allowed:

  • residue number (including insertion code)
  • residue number list and range
  • molecule number
  • union operator |

For instance, selection 1/1,2,5:7|2/-1,2A includes residues with numbers 1, 2, 5, 6, and 7 of the first molecule and residues with numbers -1 and 2A of the second molecule.