Efficient algorithm for conformational search of macrocyclic molecules

This thesis describes a new algorithm for conformational search of macrocyclic molecules. It scans a large number of candidate conformations and minimizes only the promising ones. These candidates can be generated by two operators that construct new conformations from known minima. The candidates have similar bondedinteraction energy as the known minima and possibly lower non-bonded interaction energy. This algorithm is 9 to 11 times faster than the existing methods when tested on two large rings, cycloheptadecane and rifamycin SV. Thesis Supervisor: Tomis Lozano-P6rez Title: Professor, Electrical Engineering and Computer Science