Author: OneAngstrom

If you’ve ever tried to animate a molecular simulation and watched your region of interest drift out of frame, you’re not alone. This is a common challenge in molecular modeling when dealing with complex systems—especially when atoms of interest move…

One of the challenges molecular modelers often face when exploring chemical space is deciding where to modify a molecule. Minimal changes at the right location can significantly influence a molecule’s properties—whether you’re optimizing binding affinity, altering pharmacokinetics, or reducing toxicity.…

When working on complex molecular systems, navigating between different spatial regions, projections, or zoom levels becomes a frequent task. Whether you’re analyzing a protein pocket in close detail or comparing macromolecular quaternary structures, this back-and-forth can be tedious and time-consuming.…

When modeling complex molecular systems, it’s easy to take one step too many — a misplaced atom, an unintended bond, or even unintentionally overriding valuable data while trying to perfect your structure or simulation setup. The challenge? Rebuilding what you…

Defining the binding site in protein-ligand docking is one of the most crucial — and sometimes tedious — steps in early-stage molecular modeling. If you’re working with a protein structure that already includes a bound ligand, you might wonder why…

Starting a new molecular modeling project often means spending a lot of time tweaking visual representation settings. If you’ve ever wished there was a way to accelerate this part of your workflow while still producing high-quality, beautiful images, visual presets…

Superimposing protein structures to compare their folds or map conserved regions is a common task in computational biology. But doing it manually—whether with PyMOL scripts or rigid RMSD calculations—can be repetitive and error-prone. If you’re spending time writing custom scripts…