BioSim Talk #7

(An IPR seminar series supported by WPI PRIMe and ASPiRE)

Date: November 1, 2024 (Fri)
Time: 4:00 – 5:30 pm
Venue: 2F Conference Room (#202), Institute for Protein Research,
Osaka U. (Suita Campus), +Zoom
[Meeting ID: 821 3683 8780 / Passcode: 762776]

Please inform us if you will be participating online or joining our slack
sandhyatiwari[at]protein.osaka-u.ac.jp, shinobu.ai.prime[at]osaka-u.ac.jp (Please replace [at] with @.)

DOWNLOARD THE FLYER HERE

Multicanonical Molecular Dynamics (McMD) based dynamic docking is a powerful tool to not only predict the native binding configuration between two flexible molecules, but it can also be used to accurately simulate the binding/unbinding pathway. Furthermore, it can also predict alternative binding sites, including allosteric ones, by employing an exhaustive sampling approach. Since McMD-based dynamic docking accurately samples binding/unbinding events, it can thus be used to determine the molecular mechanism of binding between molecules. In this talk | will showcase various applications of McMD-based dynamic docking, applied to small ligands, medium-sized ligands, peptides to their receptors, as well as protein-protein docking.

Finally, I will demonstrate how anyone*** can perform McMD-based dynamic docking simulations, by showcasing the dynamic docking between MDM2 and a medium-sized compound, including all the steps involved in preparing the system, executing the simulations and analyzing the results.

*** NB: you do need to have a desktop/workstation/server/cluster (don’t do this on a laptop/phone)