One commonly overlooked yet crucial step in modeling protein conformational transitions is setting up the sampling box. If you’ve struggled with generating relevant pathways or wondering why you’re getting unexpected motions, it’s likely that your sampling region is not well…

When building molecular models, effective visual distinction between different structures, chains, atoms, or datasets is essential for clarity. But how often have you found yourself stuck with default colors that just don’t work — whether they’re too similar to distinguish…

Finding ligand unbinding pathways can be complex, especially when accurate energy evaluations are essential to guide the search. If you’re using SAMSON’s Ligand Path Finder, correct setup of the energy model is a critical early step. In this post, we’ll…

In molecular modeling, creating smooth and accurate visualizations of molecular transitions is often a challenge. Whether you’re investigating protein-ligand interactions or large conformational changes in biomolecular complexes, understanding the path a molecule takes between two states can be essential for…

Creating animations of molecular structures is not just about aesthetics—it’s a powerful way to communicate behavior, mechanisms, and design insights. But for many molecular modelers, translating molecular motions into effective animations can be time-consuming and unintuitive. One frequent challenge: how…

Handling complex molecular selections is a routine — and often tedious — task for molecular modelers. Whether you’re toggling between ligands, protein domains, cofactors, or solvent molecules, it’s easy to lose precious time reselecting the same groups over and over.…

Molecular modelers often find themselves repeating tedious scripting tasks—especially when moving or manipulating atoms in 3D space. Whether you’re prepping a structure for simulation, analyzing trajectories, or coding interactions, it all adds up. What if you could just explain what…

Creating molecular animations can be a powerful way to communicate complex structural transitions, conformational changes, or step-by-step molecular mechanisms. However, when presenting these animations, it’s often necessary to slow down or emphasize a particular moment in the animation. For instance,…

One common challenge in protein-protein docking is the overwhelming number of possible orientations to explore. Each additional degree of rotational freedom can substantially increase docking time and the likelihood of false positives. Fortunately, you can reduce these issues by constraining…

Understanding how ligands bind to proteins is at the core of molecular modeling and drug design. But when the complexity of a 3D structure makes it difficult to spot key interaction patterns, zooming out to a clean, clear 2D representation…