Hit Determination

Within BMaps hit determination is currently available in two forms. The first is the recognition of hot spots on the protein, and the second is the examination of strongly interacting fragments at those hot spots. The below outlines the practical aspects of performing these two tasks.

What are Hot Spots?

Hot spots, as described in our publication, are positions on a protein where:

(i) Fragments are found to have favorable free-energy interactions with the protein

(ii) This favorability is found to be true across a set of chemically diverse fragments

(iii) Tightly bound waters are not blocking fragment binding that otherwise might appear to achieve high affinity.\

These hot spots are useful for identifying active sites, testing druggability, finding allosteric sites, and finding sub-pockets within orthosteric sites. With active sites clearly defined, libraries of potential hit compounds can be docked to the active site or fragment simulations can determine strongly interacting fragments from which hit compounds can be grown.

Hot Spot Simulations

Hot spot simulations, like water and fragment simulations, can be accessed through the Modeling Tasks button on the BMaps sidebar. Hot spot simulations are currently run using a set of 16 diverse clustering fragments. After setting up the simulation settings, which are described in more depth here, you can prepare the system and go to the simulation shopping cart. You will notice that the shopping cart is repopulated with the 16 fragment diversity set.

It is not recommended to remove any of these fragments unless you are sure you know what you are doing. Note that if you do change the fragments then the hot spots will not be directly comparable to the precomputed hot spots provided in BMaps. Updating which fragments are used for hot spot simulations can also be performed in the Fragment Manager using the "In Hotspots" column.

Also note that hot spot simulations are a combination of fragment maps and thus will show up in the Job Summary panel as such.

Visualizing Hot Spots

As noted in the Visualization section, the calculated hot spots can be visualized through the Interaction Highlights button on the side bar. Specific hot spots can be shown or hidden using the Protein tab of the Selector menu and scrolling to the Hotspots header. The information circles can be hovered over to show the average excess chemical potential of the fragments at that spot on the protein. All other Selector menu buttons operate the same as described in the Menus section. 

Hot spots in the 3D work space appear as numbered clouds.