molBLOCKS: decomposing small molecule sets and uncovering enriched fragments

Summary: The chemical structures of biomolecules, whether naturally occurring or synthetic, are composed of functionally important building blocks. Given a set of small molecules—for example, those known to bind a particular protein—computationally decomposing them into chemically meaningful fragments can help elucidate their functional properties, and may be useful for designing novel compounds with similar properties. Here we introduce molBLOCKS, a suite of programs for breaking down sets of small molecules into fragments according to a predefined set of chemical rules, clustering the resulting fragments, and uncovering statistically enriched fragments. Among other applications, our software should be a great aid in large-scale chemical analysis of ligands binding specific targets of interest. Availability and implementation: molBLOCKS is available as GPL C++ source code at http://compbio.cs.princeton.edu/molblocks. Contact: mona@cs.princeton.edu Supplementary information: Supplementary data are available at Bioinformatics online.