This is a screenshot from my webservice MAHORI. The service has an aim to assist fragment-based inhibitor design. It is a bit complicate to use and therefore I create a video from a screen capturing program.

The idea is that similar chemical fragments in the binding pocket of proteins should make contact to similar atomic environment. If you choose the set of hetero-atoms that can influence the binding, you will find that they form similar numbers of interactions in various pockets.

The example illustrates the use of staurosporine’s N4 and O6 atoms, which forms similar number of interactions among various kinases. If you have a fragment of interest, you can put those fragments to look for the existing environment in the Protein Data Bank. Maybe those outputs resemble your pocket of interest.

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