Presenting molecular models to colleagues, students, or during talks can often lead to a common issue: overwhelming your audience with too much structural detail all at once. When atoms and bonds appear simultaneously, even well-prepared presentations can become visually confusing,…

In molecular modeling, showing how ligands bind to receptors is key when presenting your research. But visualizing this interaction clearly and smoothly can quickly become time-consuming. If you’ve ever struggled with showing how a molecule docks into a protein pocket…

Molecular modelers often know what they want to show, but not how to show it. When presenting complex molecular assemblies or dynamic motions, a static image or even a simple rotation often doesn’t do justice to the structure’s spatial features.…

Modeling membrane proteins realistically often hinges on embedding them within a lipid bilayer. But placing lipids manually around a protein system can be time-consuming, potentially error-prone, and quite repetitive for simulations involving different lipid types or membrane compositions. Fortunately, Molecular…

One of the common challenges in molecular modeling — whether you’re analyzing proteins, designing nanosystems, or preparing presentations — is clearly communicating what you’re seeing. At the atomic and molecular scale, raw geometry and topology data can quickly become hard…

When exploring large-scale conformational changes in proteins, molecular modelers often face the same bottlenecks: visualizing smooth transition paths is time-consuming, and most available tools either require heavy computation or offer limited interactivity. This can slow down studies related to conformational…

One of the most common but often underestimated sources of errors when preparing molecular systems for coarse-grained simulations is improper residue and chain numbering. This becomes especially important when working with multiple copies (or replicas) of a protein in a…

If you’ve ever worked with large sets of protein structures—from databases like the PDB or in-house experimental data—you already know how time-consuming the preparation step can be. Downloading structures, checking for missing atoms, stripping unnecessary molecules, adding hydrogens… doing it…

One of the most common pain points for molecular modelers starting with protein docking is the setup of the system. Performing docking without carefully preparing your molecular models can lead to wasted computing time and misleading results. If you’ve ever…