Author: OneAngstrom

For molecular modelers working on viral proteins, computing conformational transitions between known structures is a frequent challenge. Whether designing potential inhibitors, studying viral entry, or simply trying to understand structural dynamics, one practical problem remains: how to interpolate between two…

Creating clear and engaging scientific animations for molecular design can be a challenge, especially when you want to convey not only structural information but also guide your audience through a story. One often overlooked aspect that can improve the clarity…

When studying the dynamic behavior of molecules, it’s common to want the camera to stay focused on a certain region — a binding site, an atom group, a functional group in motion — while the rest of the molecular system…

If you’re a molecular modeler preparing visual materials for teaching, a research presentation, or a publication, you’ve likely struggled to clearly communicate the internal architecture of complex molecular assemblies. It’s common to want to highlight specific subunits or depict how…

When exploring ligand unbinding pathways in molecular modeling, one common frustration is the unrealistic movement of either the ligand or the protein during simulations. If you’ve found your protein drifting along with the ligand or noticed unnatural trajectories, the problem…

Molecular modelers often face the challenge of jumping between different tools and platforms to complete different parts of their workflows. Running an optimization in one tool, visualizing it in another, and writing custom scripts to connect them can slow down…

Running molecular simulations can be demanding on your computer, especially when using software like GROMACS. If you’ve ever tried to run a local job and found your system nearly unusable during the simulation, you’re not alone. This is a common…

When creating molecular presentations or simulations, one common frustration among researchers and modelers is realizing that the changes in atomic positions — carefully crafted through movements, docking steps, or simulations — are not thoroughly documented or not reproducible when returning…