Protein-ligand docking is only half the story. Once a docking run completes successfully, understanding how your ligand interacts with the receptor is critical — not only to validate the result, but also to extract meaningful insights. That’s where visual analysis…

One of the most time-consuming tasks in molecular modeling is selecting specific atoms according to their properties. Whether you’re preparing a simulation, cleaning up a structure, or visualizing a region of interest, selecting the right atoms quickly and precisely is…

In molecular modeling and communication, clarity is critical. Whether you’re preparing a presentation for colleagues or publishing a video abstract, showing a complex molecular structure all at once can be overwhelming for your audience. Often, you want to guide the…

A common challenge for molecular modelers when creating visual narratives or science presentations is controlling exactly when molecular structures appear in an animation. Whether you’re showcasing a complex assembly process, a ligand binding sequence, or a molecular revelation, precise timing…

Animations can be a remarkably effective way to communicate complex molecular mechanisms, structural changes, or simulation data — especially in presentations or publications. But for many molecular modelers, creating animations still sounds like a time-consuming or technically difficult task. If…

If you’ve ever tried to move a group of atoms in your molecular model, only to realize that they’re no longer in the same geometric arrangement, you’re not alone. Many molecular modelers face this issue when managing atomic coordinates for…

Anyone who has worked with complex molecular systems knows that managing atomic structures, ligands, simulations, and annotations can quickly become overwhelming. As molecular modelers, we often lose precious time searching for that one piece of structural data buried deep in…

One of the most common sources of errors during molecular dynamics simulations happens right at the start: providing the wrong input file. Whether due to typos, incorrect paths, or confusion between file types, this early mistake can become a frustrating…

Automatic symmetry detection in molecular structures can be a huge time-saver. But if you’re working with large biological assemblies, such as viral capsids or protein complexes with ambiguous layouts, automated tools might suggest several plausible symmetry groups. For structural biologists…