BioSim Talk #7

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

Date & Venue

• Date: Friday, November 1, 2024, 16:00 – 17:30
• Venue: 2nd Floor Medium Conference Room, Institute for Protein Research (Suita Campus, Osaka University) + Zoom
• Zoom: If you would like to join via Zoom, please contact us at the addresses below.
  Meeting ID: 821 3683 8780
  Passcode: 762776

Presentation Information

Title: Dynamic docking using Multicanonical MD

Speaker: Gert-Jan Bekker, PhD.
Specially Appointed Assistant Professor (Lecturer)
PDBj & Laboratory for Protein Crystallography

Abstract

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 I 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)

All are welcome!

Contact

Sandhya P. Tiwari
Email: sandhyatiwari[at]protein.osaka-u.ac.jp (Please replace [at] with @)

Ai Shinobu
Email: shinobu.ai.prime[at]osaka-u.ac.jp (Please replace [at] with @)