Molecular Modeling and visualization have gone hand in hand over the decades. They help us understand the molecular systems we work with and correctly prepare the systems for simulation — there’s nothing worse than running a simulation for months and then finding out we missed an important protonation state or other small detail. But, don’t worry too much if it happens — we have all been there! 🙂
Describing your system
Gareth Denyer of U of Sydney recently introduced me to sketchfab. It is a great way for sharing your system of interest in a responsive 3D visualization, with comments describing specific points you want to highlight. This is a very responsive tool for 3D in general, so it does not have the functionality of typical visualization software, but it allows users to just open a browser and follow your explanations.
Cell Paint: David Goodwill does some of the most beautiful molecular paintings I have seen, and their software allows us to participate on the process of drawing cells and viruses.
My group and I have been impressed with the immersive experience we get in a VR environment and the insights it is providing. We have been using Nanome to navigate our preferred PDB codes in ways previously unknown to us — it is very intuitive and has great functionality to rotate bonds, scale, and design/mutate proteins and nucleic acids.
We have been using Peppy developed at the University of Sidney to model peptide systems. It has a nice aspect of molecular modeling toolkits — but scales so well to the size of peptides. It even has a force field that you can run MD on while you explore the peptide’s conformations, it’s ability to adopt hairpin or helical conformations… it brings insight into molecular interactions.
VMD: good for trajectories, rendering, exporting into 3D programs and analysis — I have used this one the most.
Chimera: beautiful presets for rendering, great for static structures and cryoEM modeling.
PyMol: one of the first I worked with, some of my former group buddies loved it!
Mol*: pretty new web-based visualization. It’s worth a try!
High School Research Experience Using VR
Julie and Grace joined our lab for 8 weeks through the CPET program. They learned about molecular systems we study related to cancer using virtual reality.