Author: OneAngstrom

If you’re working with molecular docking, structural analysis, or simulations across many proteins, you’ve likely run into this challenge: preparing dozens or even hundreds of raw PDB files manually. Stripping water, removing unnecessary ligands, adding hydrogens, resolving alternate locations… doing…

Many molecular modelers and structural biologists face a recurring challenge: how to clearly communicate docking processes in presentations or teaching materials. Static images often fall short when trying to illustrate the journey of a ligand towards its receptor. Wouldn’t it…

Understanding how proteins change shape between two conformations is a challenge faced by many molecular modelers. These conformational changes are essential for protein function, but identifying plausible transition pathways and analyzing their energy profiles can be time-consuming and complex. The…

Anyone who has spent time designing or simulating molecular systems knows the frustration of making a change—perhaps moving an atom, deleting a node, or applying a modification—only to instantly realize it wasn’t the right move. In larger or more complex…

Creating molecular animations isn’t just about rotating a molecule or changing colors. Sometimes, it’s about storytelling — visualizing interactions, processes, or transitions in ways that make complex behavior simpler to understand. One frequently overlooked but highly effective animation technique in…

If you’ve ever felt like your molecular presentations look a bit static or lifeless, you’re not alone. Many molecular modelers and educators wish they had better ways to visually showcase the 3D nature of molecular structures without spending hours editing…

Molecular modelers often face a critical challenge when it comes to reproducibility and performance of molecular dynamics simulations. If your workflows rely on a customized or system-specific build of GROMACS—for example to support consistent academic publishing or ensure compatibility with…

In scientific animations, clarity of communication is crucial — especially when you’re trying to explain molecular structures, transitions, or reaction mechanisms. One challenge that often comes up in molecular modeling is how to control the appearance of specific molecular elements…