Explore Binding Sites
SiteMapper is a free web server for binding site comparison based on residue match and deviation minimization. Taking two user defined binding sites as reference and fitting structure, SiteMapper try to align these two structures in order to obtain a correspondence between residues from reference site and fitting site and evaluate the similarity between these two binding sites. SiteMapper can be very useful for evaluating the binding site similarity or performing discontinuous sequence alignment for binding sites.
To use SiteMapper, simply enter a PDB code for reference structure and fitting structure, then the corresponding protein structures will be loaded along with the bound ligands. Next, you can define the binding site by choosing a ligand and provide a distance cutoff to include all residues within that cutoff to represent a specific binding site. You can also select or deselect residues to refine a binding site. Finally, click "submit" to submit the job. After a short period, the result will be rendered, including the spacial position of the aligned binding sites, residue correspondences and a numerical score measured the similarity.
HERE is a precalculated example!