Molecular modeling often involves navigating between abstract representations, such as sequences, and the tangible three-dimensional structures they correspond to. This can be disjointed: selecting residues in a sequence viewer may not reflect immediately in your 3D modeler, or vice versa.…

Editing molecular systems during a simulation is something many computational chemists and structural biologists wish they could do more freely. Unfortunately, traditional force fields assume fixed topologies, making dynamic changes — like the formation or breaking of covalent bonds —…

When modeling conformational changes in proteins, one of the most common challenges is finding plausible transition pathways between different conformations. It’s especially valuable when you have experimentally resolved structures representing both the start and goal conformations, but no information on…

Designing DNA nanostructures can be both inspiring and time-consuming. Whether you’re creating wireframes, nanotubes, or lattice-based geometries, designing similar components repeatedly across projects can become tedious. This is where component saving in Adenita becomes particularly useful: it allows you to…

If you’ve tried making sense of molecular data in 3D, you know how fast your screen can turn into a tangled visualization that’s difficult to interpret. Whether you’re exploring structural models or protein properties, the way colors are applied can…

When working with dynamic molecular trajectories, such as protein-ligand interactions or conformational changes, it’s easy to lose sight of the region you care about. As structures evolve, atoms drift, and camera positions remain fixed, researchers often end up missing the…

When setting up molecular simulations, especially with GROMACS, getting the selection of atom groups right is essential for accurate results and efficient analysis. This is where custom index groups come into play — a feature that can save you time…