Author: OneAngstrom

Protein-protein docking is one of the cornerstones of structural bioinformatics, but it can be computationally expensive – especially when conformational sampling is performed across broad orientations. One way to make docking significantly faster and more relevant is to limit the…

When working with complex molecular systems, it can be overwhelming to dig through countless properties just to make a small adjustment. Whether you’re modifying atom positions, checking chemical features, or exploring the hierarchy of nodes in your system, the ability…

Creating consistent and clear molecular illustrations can quickly become tedious when you have to manually adjust representations, colors, and rendering options every time. Whether you’re preparing multiple images for a publication, setting up visuals for a presentation, or just trying…

When studying molecular interactions, especially the dynamics of ligand binding and unbinding, one common challenge faced by computational chemists and modelers is the need to extract atomic coordinates along specific paths of motion. This data is crucial for generating reaction…

Understanding the conformational changes in viral proteins is crucial when you’re designing inhibitors, vaccines, or simply trying to comprehend viral infectivity mechanisms. One typical challenge for molecular modelers and computational biologists is visualizing these transitions effectively. Static structures in the…

Working with carbon nanotubes (CNTs) often requires precise 3D modeling tools, and for many molecular designers, building such models from scratch can be time-consuming and unintuitive. Especially when testing different chiralities or designing multi-walled CNTs, it’s important to go from…

When creating molecular animations, timing plays a crucial role in maintaining audience engagement and clearly communicating what matters. Fast transitions between frames can confuse viewers or cause them to miss critical details. What if you need your audience to absorb…

Setting up a production molecular dynamics (MD) simulation often begins with a series of tiny decisions that can greatly affect both results and simulation stability. For many molecular modelers, selecting the correct input files and simulation parameters becomes a repetitive…

Creating clear, consistent visuals of molecular systems can be a tedious task, whether for scientific communication, teaching, or just keeping track of complex simulations. The common workaround involves repeatedly adjusting representations, color schemes, visibility settings, zoom levels, and more —…