We'd like to introduce a new member of the Omnia ecosystem, YANK. YANK is an OpenMM-powered Python code for performing alchemical binding free energy calculations to compute small-molecule binding affinities to biomolecules, as well as an open platform for experimenting with new algorithms to make this process reliable and efficient. YANK provides convenient tools for setting up binding affinity calculations between proteins and small molecules.
YANK is able to take advantage of one of the more exciting aspects of OpenMM---namely, its ability to run incredibly fast implicit solvent calculations. In a paper we recently published in JCAMD, we used this feature to show how multiple binding sites and accurate free energies could be obtained for small molecule ligands of the T4 lysozyme L99A model binding system from Brian Shoichet and Brian Matthews. Input files for this system will be available as one of the examples distributed with YANK.
Right now, YANK is still being tested in its final phases before a first public release, but stay tuned for further updates!
Learn more about YANK at our GitHub page.