Find chemical

This form can be used to search for Pocketome entries with ligands similar to the given chemical.

Similarity cutoff (0.–1.):

Chemical search can be performed in several modes with self-explanatory names. The default cutoff (0.7) corresponds to a reasonable similarity. It can be increased to 0.9 for very similar compounds or decreased to 0.6 for a more inclusive search. In the substructure and exact modes, the search also might consider the similarity metric to find the most relevant hits.

Chemical search is performed within chemical indices obtained from all the Pocketome entries. PDB structures often have missing heavy atoms, so two indices were constructed: (i) the ideal index that represents chemical structures from residue libraries, and (ii) the PDB-based index. In most cases, both indices contain nearly the same chemicals, except for molecules with covalently bonded heteroatomic residues that (due to non-standard connectivity) only present in the PDB-based index.