Automated structure design in 3D

A system is being developed, based on structure generation methods, for the design of molecules to fit a variety of constraints. The system is modular and uses techniques from artificial intelligence to solve general problems in molecule design. Heuristics are being developed based, in part, on the different kinds of constraints that might be available to the system, e.g., the shape and electrostatic nature of a cavity. The heuristics are then used to restrict the combinatorial explosion that is inherent in structure generation. The program has been tested using the appa binding site of Trypsin and a range of different structures that fit the site have been generated. Some of these structures are very closely related to appa and the predictive value of the program has also been demonstrated.