iMD-VR for flexible protein-ligand docking

GS-neuraminidase.gif

Becca Walters undocks & redocks the flu drug oseltamivir (tamiflu) into the binding pocket of the neuramanidase protein

We’ve just published a paper describing the use of interactive molecular dynamics in virtual reality (iMD-VR) for carrying out flexible protein-ligand docking, demonstrated through experiments carried out docking drug molecules into the binding pockets of trypsin, neuraminidase, and HIV-1 protease.

A major aim of the work was to investigate whether iMD-VR tools afforded sufficient control for users to accurately carry out the detailed atomic manipulations required to dock flexible ligands into dynamic enzyme active sites and recover crystallographic poses. The results show that both iMD-VR experts and novices alike were able to recreate respective crystallographic protein-ligand binding poses within 5–10 minutes – and the majority were able to recover binding poses within 2.15 Å RMSD of the crystallographic binding pose!
These results suggests that iMD-VR offers an interesting new approach for simulating drug docking and generating binding hypotheses.

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