Fragment joining

In the BROOD GUI, it is possible to load two fragments and use the brood -linkOnly search to identify potential linkers that can join the fragments with an energetically favorable, medicinally relevant linker in a low-energy conformation. This search can be carried out in a protein’s active site, taking account of the need for the linker to fit into the active site as well as join the fragments. For more information on this application, please see the tutorials section.

Cyclization

Long-distance cyclization, like fragment joining, is about finding a chemical fragment that can bridge to moieties given a particular 3D orientation. Use the brood -linkOnly option for long-distance cyclization.