BioExcel Webinar #82: Cryo-EM structure refinement with density-guided simulations in GROMACS

Date: March 4th, 2025, 15:00 CEST / 16:00 EEST

Abstract:

Refinement of an initial atomistic model into a target density map is one of the key steps in cryo-EM structure reconstruction. Density-guided molecular dynamics is a widely used approach for this purpose, helping to balance physical plausibility of the model and fitting scores. In this webinar, I will provide an introduction to the density fitting functionality in GROMACS, demonstrate you a basic use-case example, and discuss available settings. I will also share density fitting results for several diverse protein systems.

Duration: 1 Hour

Webinar will be hosted on ZOOM (install the latest Zoom application before the webinar via https://zoom.us/download)

Presenters

Tatiana Shugaeva is a PhD student in Erik Lindahl’s group at KTH Royal Institute of Technology, Stockholm. She is involved in developing cryo-EM structure refinement methodologies using density-guided molecular dynamics simulations. Her research is also focused on the molecular mechanisms underlying the function of pentameric ligand-gated ion channels. In 2020–2022 Tatiana studied F-type bacterial ATP synthases in Boris Feniouk’s group at Lomonosov Moscow State University. At the same time, she contributed to projects at BIOCAD, a pharmaceutical company, where she worked on improving antibody affinity and modelled AAV capsid structures for gene therapy applications.

BioExcel, the leading European Centre of Excellence for computational biomolecular research, aims to support Life Science academic and industrial researchers in the effective use of HPC biomolecular s