When setting up molecular dynamics simulations, especially with approximately spherical molecules in solution, most modelers focus heavily on force fields and solvent types. Yet, there’s an often-overlooked choice that can bring significant performance benefits: the shape of the unit cell…

Exploring the effects of small chemical modifications on a lead compound is a daily task for many molecular modelers, particularly when optimizing a series of analogs for desirable properties like potency, selectivity, or ADMET characteristics. However, this form of structure-activity…

Molecular modelers often face the challenge of presenting their work in a clear and intuitive manner. When creating animations of molecular systems—whether for presentations, publications, or teaching—controlling *when* specific atoms or groups become visible is essential. Flickering atoms or unclear…

Animations are a powerful way for molecular scientists to communicate complex structures and phenomena clearly. Whether you’re teaching molecular docking, showcasing a simulation, or presenting a structural transformation, effective animations save time and help others understand your work faster. But…

Creating effective visual presentations of molecular systems can be time-consuming. One common challenge molecular modelers face is clearly showing how individual components of a complex structure come together. Whether preparing figures for a paper or animations for a presentation, clearly…

When modeling molecular systems, a recurring frustration among researchers is having to remeasure distances, angles, or torsions each time the system changes or is reopened. Whether you’re analyzing bond lengths after a minimization or monitoring torsion angles in a conformational…

Refining protein structures can be inefficient when outlier residues fall outside allowed conformations in a Ramachandran plot. If you’ve ever opened a homology model or experimental structure only to see white dots far from the safe yellow zones, you know…

Understanding how ligands move within and around proteins is essential for interpreting molecular dynamics simulations and gaining insights into unbinding mechanisms. However, with the large number of atoms and data points in simulations, the movement of the ligand as a…