molBLOCKS: decomposing small molecule sets and uncovering enriched fragments

    loading  Checking for direct PDF access through Ovid

Abstract

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.

Related Topics

    loading  Loading Related Articles