Not all potential inter-fragment connections are equally
druglike. Increasing the probability of druglike
connections will improve the efficiency of the algorithm.
Ring-formation is an important example. Unbiased
random IC/non-IC connections do not reflect druglike chemistry
(this is an argument for reaction-based library enumeration).
One solution is to use ringsystems as fragments. In addition
to FRAGs and CFRAGs, ringsystems can be used as fragments.
Ringsystems with IC attachments are included as CFRAGs,
those with non-IC attachments are included as FRAGs (ringsystems
may be both).
Daylight Chemical Information Systems Inc.
