BioSM is a cheminformatics tool that uses known mammalian biochemical compounds (scaffolds) and graph matching methods to identify biochemical structures in chemical structure space. BioSM provides a qualitative (yes/no) and quantitative (ranking) method for biochemical annotation of chemical space, and thus will be useful in the identification of unknown biochemical structures in metabolomics and other life science applications.
BioSM is written in Java and can be run on any platform with a Java virtual machine. Execution scripts for Windows and Linux are bundled along with the Java archive in the zip file below.
Acknowledgment and Disclaimer
This material is based upon work supported in part by Grant 1R01GM087714 from NIH, Grant No. IIS-0916948 from NSF, the Agriculture and Food Research Initiative Competitive Grant No. 2011-67016-30331 from the USDA National Institute of Food and Agriculture, and the Booth Engineering Center for Advance Technology (BECAT) at the University of Connecticut. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the funding agencies.