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

SUBMITTER: Graham SE 

PROVIDER: S-EPMC6186161 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature