Workshop in the MIDST of Modeling Membrane Embedded Proteins and Ligand Transport
Sabanci University - Altunizade Campus, Istanbul, Turkey
November 30, 2025
In the theory session, we will introduce the fundamentals of molecular dynamics (MD) simulations of membrane proteins and focus on the principles of steered molecular dynamics (SMD), including how external forces are applied to explore conformational changes or molecular transport through biological channels. We will discuss how to set up protein–membrane systems and how to interpret SMD force profiles and potential of mean force (PMF) results. In the hands-on session, we will perform MD and SMD simulations of a membrane-embedded protein to observe the passage of a small molecule through the pore. The exercises will include system building, equilibration, and analysis using CHARMM-GUI, NAMD, and VMD software.
Level: Participants are expected to have minimal experience with MD simulations of proteins or similar systems
