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.