Comparisons of Molecular Structure Generation Methods Based on Fragment Assemblies and Genetic Graphs

The use of quantitative structure–property
relationships
(QSPRs) helps in predicting molecular properties for several decades,
while the automatic design of new molecular structures is still emerging.
The choice of algorithms to generate molecules is not obvious and
is related to several factors such as the desired chemical diversity
(according to an initial dataset’s content) and the level of
construction (the use of atoms, fragments, pattern-based methods).
In this paper, we address the problem of molecular structure generation
by revisiting two approaches: fragment-based methods (FMs) and genetic-based
methods (GMs). We define a set of indices to compare generation methods
on a specific task. New indices inform about the explored data space
(coverage), compare how the data space is explored (representativeness),
and quantifies the ratio of molecules satisfying requirements (generation
specificity) without the use of a database composed of real chemicals
as a reference. These indices were employed to compare generations
of molecules fulfilling the desired property criterion, evaluated
by QSPR.