Date: 4 March 2025
Time: 15:00 CET
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.
Presenter
Tatiana Shugaeva, KTH
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.
