Customizable and Automated Scientific Molecular Rendering with Molecular Nodes
As molecular simulations and other molecular entities continue to grow in scale and complexity, there is an increasing demand for flexible, high-quality visualization tools capable of handling these complex datasets efficiently. Molecular Nodes enables quick import and visualization of structural biology data inside of Blender, a free and open-source 3D computer graphics software tool. Blender has proven to be an innovative platform, providing versatile and industry-quality renderings of static molecules, molecular dynamics (MD) simulations (with the support of MDAnalysis), cryo-EM density maps, and EM tomography. It has become the go-to package for both experimentalists and computational scientists, widely used to create cover images and striking illustrations for academic and outreach purposes, including recent high-profile projects like the AlphaFold 3 release video by Google DeepMind.
Molecular Nodes is currently designed with a graphic user interface (GUI) workflow being the main input method. This limits the ability and uptake by computations chemists and biophysicists who quite often work in headless computational environments. Reusability and reproducibility are also concerns in an effort to include Molecular Nodes in more computational pipelines with FAIR principles in mind.
GGMolVis provides a streamlined, object-oriented API for molecular visualization, inspired by the design philosophy of Matplotlib and ggplot2. Such an API would enable users to achieve automated, customizable visualizations with just a few lines of code, and allow platforms like Molecular Dynamics Data Bank (MDDB) and Protein Data Bank (PDB) to produce large-scale renderings of their molecular archive, leveraging the most up-to-date rendering technologies that Blender provides.