[AMBER] Efficient, accurate estimation of relative binding free energies

From: Guo, Zhuyan <zhuyan.guo.merck.com>
Date: Mon, 30 Jun 2014 08:13:50 -0400


We are interested in methods in efficient, accurate estimation of relative ligand binding free energies that quickly rank/priorities compounds in congeneric series such as in a lead optimization paradigm in drug discovery. One example of such techniques is the L-dynamics method that can evaluate multiple ligands simultaneously from a single MD run. It is currently implemented in CHARMM. Here is a reference to most recent work from Dr. Brooks' lab at the University of Michigan:

Knight JL, Brooks CL, III. Multisite Dynamics for Simulated Structure-Activity Relationship Studies. J. Chem. Theo. Comput. 2011;7(9):2728-39

Has anyone ported L-dynamics to AMBER or know of similar code for the AMBER platform?

Please let me know if you have any information or are interested. Thank you!

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Received on Mon Jun 30 2014 - 05:30:02 PDT
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