BPS2023 was full of amazing posters, talks and workshops! On any given day the schedule was so packed with interesting content that it could be hard to choose what to attend, though I didn't regret any of my choices. As a sample of my Tuesday at the conference I'd like to talk about a workshop and two posters that were memorable to me and that share as a common thread the Martini force field - a set of parameters used to describe interactions between atom groups in particle-based molecular simulations, such as molecular dynamics simulations.
Let me start with these two cool posters I saw on Tuesday afternoon:
The onset of whole-cell modeling using the Martini force field by Jan A. Stevens: Just from its title, I was expecting to see a cool project. It really was. Jan presented their ongoing efforts on constructing a whole-cell model at a molecular resolution. Surely, the model involves some simplification of the cell composition, but it is an enormous step toward more realistic modeling of complex phenomena! Want to read more about it? They even published a paper on this project here.
The Martini 3 ecosystem for coarse-grained simulations by Fabian Grunewald: Again, as a computational biophysicist who has been using coarse-grained modeling, I had to see this poster. Fabian presented the Martini Database, all of the scripts and tools developed by the Martini developers, tutorials and even information on how to learn and ask for help. I loved the amazing visuals in the poster. In addition to that, listening to Fabian on their ongoing efforts to help people learn and use these tools was really impressive.
Later on the same day, the Computational Modeling of Binding Thermodynamics session started at 7:30 PM. The first workshop was by far my favorite!
Protein-ligand binding with Martini 3 by Dr. Siewert Marrink: Protein-ligand binding can be studied computationally using molecular modeling in which biomolecular systems’ components such as a protein, ligand and solvent are described as particles. Binding studies often use all-atomistic modeling; each particle represents a specific atom type with properties such as atomic mass, radius, and (often fixed partial) charge. In coarse-grained modeling, particles represent a group of atoms. The interactions between the particles of a biomolecular system can be computed using a set of parameters for all particle types. The set of parameters is also called a “Force Field”. Martini is the most popular force field for coarse-grained modeling especially for studies involving membrane proteins.
Dr. Marrink started the workshop by explaining clearly how the Martini 3 force field works. To answer why we need coarse-grained modeling, he had a straightforward answer: Martini 3 has excellent computational efficiency － it allows us to run simulations of much larger systems for a much longer time. He then demonstrated example systems where protein-ligand binding sites, pathways and binding free energies were accurately predicted with Martini 3. My take-home message from this workshop was that Martini 3 can be used to study protein-ligand binding even in cases where the binding pathway is unknown.
Overall, my Tuesday at the BPS 2023 Annual Meeting made me appreciate biophysicists who do good research as well as method development. I believe the Martini development team is also doing something even more awesome: offering open-source resources for other scientists to learn, apply and improve their tools; organizing workshops; and creating a community of biophysicists who love to study biophysical phenomena using computational approaches. I consider myself a member of this community, and their welcoming attitude and amazing resources have helped me tremendously since I started taking little steps into the Martini world.