The Matched Pairs nodes demo'd at the last SIG meeting held at Vernalis in September have just been released. See http://tech.knime.org/book/vernalis-cheminformatics-nodes#MMPs for details, or install them (v 2.10/2.11 and nightly build) and have a look. Any questions or suggestions, please let us know either via the forum or by email to knime [at] vernalis [dot] com.
Steve