H-bond network

H-bond networks and protein ensembles – SeeSAR 10.2 update

November 9, 2020 11:52

H-bond (hydrogen bond) network assessment and binding site search are introduced to SeeSAR. Again, we took that extra step and sprinkled a little magic here and there. And the work was worth the hassle: the new SeeSAR version includes addtional features and improvements to further enhance your drug discovery process.

The new H-bond network assessment provides you with even more information on your target-ligand complexes. The calculations of inter- and intramolecular H-bonds are decoupled from the HYDE assessment, enabling detailed insights into the binding of your molecule. Note that this mandates a recalculation of previously obtained HYDE scores.

The second big feature is the seamless integration of a ProteinsPlus web service from Professor Rarey’s lab at the ZBH Center for Bioinformatics (Hamburg, Germany). This new technology — called SIENA — quickly combs through all the available PDB structures to search for binding pockets similar to the one at hand. The special advantage of this technology: The comparison is not only limited to the sequence of the target alone, but additionally involves the overall topology of the binding site — which can lead to unexpected, yet valuable results. You get these comfortably aligned and ready for visual inspection now in SeeSAR.

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