Author: OneAngstrom

Molecular modelers frequently face the challenge of interpreting docking results in a way that goes beyond scores and binding poses. Visualizing the ligand environment—identifying surrounding residues, interactions, and spatial organization—is a vital yet sometimes tedious part of structure-based drug design.…

Designing carbon nanotubes from scratch can be complicated and time-consuming, especially when precise atomic alignment and control over periodicity are essential. If you’re a molecular modeler in materials science or nanotech, you’ve likely spent time manually replicating rings, adjusting rotations,…

Running molecular dynamics simulations can be a bottleneck in research workflows, especially when local computing resources are limited. Access to powerful hardware often means submitting jobs to institutional clusters or waiting in queues. But what if you could run GROMACS…

It’s common in molecular modeling to focus on how a specific part of a system behaves over time—for example, tracking the motion of a ligand inside a binding pocket or following the rearrangement of an active site in a protein.…

When preparing molecular animations for scientific presentations or teaching, clarity is key. One common challenge for molecular modelers is how to draw attention to specific components of a structure at just the right moment, without overwhelming the viewer. That often…

When working with molecular models, precise control over the position and orientation of structures is often essential. Whether you’re preparing a system for simulation, building a complex assembly, or analyzing molecular interactions, the ability to move selected components smoothly and…

One of the most common challenges molecular modelers face during protein-protein docking is handling the vast number of potential orientations and false positives generated during the search. Even when docking crystal structures, an unrestricted search can lead to misleading predictions…

Do you ever find yourself losing sight of key atoms when playing or exporting molecular animations? When tracking dynamic molecular systems, it’s common to want the camera to remain stationary while directing your attention (and the viewer’s) toward something changing…

One of the subtle but essential tasks in preparing a molecular system for a GROMACS simulation is deciding which water molecules to keep. While removing all crystal water molecules might simplify pre-processing, it may also mean losing functionally relevant water…