In molecular modeling, finding biologically relevant transition pathways between molecular states can be a challenge—especially when simulating ligand unbinding events. Often, you may already have a trajectory generated through sampling or interpolation, but need to make it more accurate from…

When preparing molecular systems for simulation, clean geometry isn’t optional—it’s essential. Poor atomic arrangements can lead to unrealistic behavior, convergence failures, or wasted compute time. That’s why optimizing geometries before launching simulations should be part of every molecular modeler’s workflow.…

When working on molecular animations, one of the most common frustrations that molecular modelers face is keeping parts of a molecule steady while the rest of the system moves. Whether you’re showcasing ligand docking, domain movement, or assembling large biomolecular…

When preparing molecular presentations, researchers often focus heavily on the scientific content—molecular structures, simulation results, docking poses—and understandably so. However, the presentation layer of that information is also crucial. Transitions that appear abrupt or distracting can reduce clarity or even…

For many molecular modelers, the ability to visualize atomic movements over time is essential. Whether you’re simulating a docking interaction, assembling molecules, or running molecular dynamics, understanding how atoms travel during a simulation is crucial. But what if you want…

Designing DNA nanostructures often involves more than just creating structures — it requires modifying them. Whether you’re untangling a strand, changing connections, or adjusting geometry, manually handling these edits can quickly become error-prone and tedious. Fortunately, Adenita, an extension of…

Have you ever shared a molecular model with a colleague or a student, only to realize later that the associated analytical Python code or visualization script didn’t make it across? Or maybe your research notes, simulation workflow, and data were…