The advantage of combinatorial chemistry
methodology is far-famed and implies the bench chemist can single-handedly prepare tens,
hundreds or thousands of compounds of known structure in the time that it would take to prepare
only a few pure entities by orthodox methodology.

There are several associated problems. The first one is how to ensure documentary support of such an approach. In particular, how to virtually "synthesize" structures as easily as they are physically synthesized. ChemoSoft removes this impediment with a toolkit described in "Generation of a virtual library" in more detail. It became apparent in ten years that single combinatorial synthesis could not appreciably improve drug design. Therefore, the challenge of how to make combinatorial synthesis smarter so as to avoid wasting money on redundant synthesis and following screening has become of paramount importance. There are two opposite (though not contradictory, but rather complimentary) answers: diverse and biased libraries. ChemoSoft has tools to design the both. They are outlined in a subsection of "Combinatorial Chemistry" called "Diversity\Similarity". The third question is how to analyze existing libraries in order to modify them without a loss in their value at least. This point is similar to that of obtaining biased libraries, though it concerns automated structure building and is depicted in "Generation of a virtual library".