MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations

Abstract

Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique for identifying binding hotspots and specific favorable interactions on a protein's surface. MixMD studies have the ability to identify these biologically relevant sites by examining the occupancy of the cosolvent over the course of the simulation. However, previous MixMD analysis required a great deal of manual inspection to identify relevant sites. To address this limitation, we have developed MixMD Probeview as a plugin for the freely available, open-source version of the molecular visualization program PyMOL. MixMD Probeview incorporates two analysis procedures: (1) identifying and ranking whole binding sites and (2) identifying and ranking local maxima for each probe type. These functionalities were validated using four common benchmark proteins, including two with both active and allosteric sites. In addition, three different cosolvent procedures were compared to examine the impact of including more than one cosolvent in the simulations. For all systems tested, MixMD Probeview successfully identified known active and allosteric sites based on the total occupancy of neutral probe molecules. As an easy-to-use PyMOL plugin, we expect that MixMD Probeview will facilitate identification and analysis of binding sites from cosolvent simulations performed on a wide range of systems.