Brannigan Lab

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Monthly Archives: November 2018

New paper in press at JCTC on implementing and interpreting ligand binding calculations

“A streamlined, general approach for computing ligand binding free energies and its application to GPCR-bound cholesterol” was just accepted to J. Chem Theory and Computation.

Alchemical free energy perturbation is a rigorous but delicate technique the lab uses frequently for measuring ligand binding affinities.  This paper has an updated and simplified approach that we’ve developed over many years.  This approach even works for non-dilute reference state or a complex, phase-separated bulk!

Is it only useful for these complicated systems? Nope! We first had to simplify many of the “usual” steps to even think about adding this complexity on top – so we’ve made the usual steps more robust, even for a protein in a dilute aqueous solution.

This paper has a lot of different pieces.  It might seem like it is a complicated paper to be advertising a simple streamlined approach!  We did need to tie multiple viewpoints and frameworks together in the paper and provide one treatment that resolved several inconsistencies. While this was a lot of work for us (and makes for a comprehensive paper), we hope using the approach and interpreting the results will be far less work for you!