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Updated: Jul 17, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
Published on: October 15, 2018
A new methodology for the simulation of flexible protein-ligand interactions
James Garner1, John Deadman, David Rhodes
1Department of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia.
Abstract:
A methodology has been developed for the simulation of induced fit between a ligand and its target protein. It utilizes constrained molecular dynamics where atoms determined to be immobile from difference distance matrix studies are fixed. Application of this methodology to HIV-1 reverse transcriptase (RT) as the example target protein has demonstrated its robustness. Short simulation times are sufficient to achieve good refinement of docking poses resulting from exchange of structurally dissimilar inhibitors between crystal structures.
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