Fast Substructure Search in Combinatorial Library Spaces

We present an efficient algorithm for substructure search
in combinatorial
libraries defined by synthons, i.e., substructures with connection
points. Our method improves on existing approaches by introducing
powerful heuristics and fast fingerprint screening to quickly eliminate
branches of nonmatching combinations of synthons. With this, we achieve
typical response times of a few seconds on a standard desktop computer
for searches in large combinatorial libraries like the Enamine REAL
Space. We published the Java source as part of the OpenChemLib under
the BSD license, and we implemented tools to enable substructure search
in custom combinatorial libraries.