A new version of SeeSAR is now available. SeeSAR is intended as an interactive tool for designing/improving ligands for drug discovery. In the SeeSAR review I write about an earlier version one of the issues I flagged was a problem when dealing with covalently bound ligands, this has now been addressed.

This version also allows such visual assessment of covalently bound ligands. They are now listed in the Molecules table together with reversibly bound ligands and co-factors. As with all the other small molecules, a focussed view showing the individual atom contributions to binding is shown in 3D when the covalently bound ligand is selected in the table. We don't, however, provide an overall binding affinity for covalently bound ligands since it is meaningless in this context.

This new version also has the the ability to choose which water molecules to consider, this way overwriting the Hyde-default in cases where you know better.