Defining the binding site in protein-ligand docking is one of the most crucial — and sometimes tedious — steps in early-stage molecular modeling. If you’re working with a protein structure that already includes a bound ligand, you might wonder why…

Starting a new molecular modeling project often means spending a lot of time tweaking visual representation settings. If you’ve ever wished there was a way to accelerate this part of your workflow while still producing high-quality, beautiful images, visual presets…

Superimposing protein structures to compare their folds or map conserved regions is a common task in computational biology. But doing it manually—whether with PyMOL scripts or rigid RMSD calculations—can be repetitive and error-prone. If you’re spending time writing custom scripts…

Generating realistic transition paths between protein conformations is valuable for structural analysis, molecular dynamics, and free energy calculations. However, a common, often frustrating hurdle in these workflows is preparing protein structures: missing atoms, extra chains, water molecules, and ligands can…

Many molecular modelers find themselves endlessly emailing large project files back and forth with colleagues. With multiple versions circulating and storage tools that aren’t tailored for research data, things can get convoluted quickly. Who has the latest version? Where did…

High-quality molecular renderings are more than just accurate representations; they’re also an important tool for communication, teaching, and research. A common challenge? Making molecules look realistic or stylized enough to effectively tell the story behind your data, while avoiding the…

When studying transitions between molecular states, a common challenge in computational chemistry is building a reliable minimum energy path connecting two conformations. This is essential for exploring reaction mechanisms, ligand unbinding, or protein conformational changes. But what’s the most efficient…

For many molecular modelers, adjusting the position of multiple atoms simultaneously is a common need — whether you’re setting up a complex structure, refining a model, or exploring conformational changes. But moving multiple nodes in 3D space without breaking the…