If you’re working with molecular systems and want to explore how a system moves between two known structures—like a bound and unbound conformation—there’s a good chance you’ve considered using the Nudged Elastic Band (NEB) method. It’s a powerful tool to…

One common bottleneck in molecular docking workflows is navigating and interpreting the results after a large-scale ligand screening run. You’ve set up your systems, launched your AutoDock Vina simulations, and now you’re left with dozens—or hundreds—of poses across multiple ligands.…

One of the most common challenges in molecular animation is conveying focus without distracting the viewer. Especially when zooming in to highlight a specific active site or molecular interaction, small shifts in camera orientation or unintended changes in depth-of-field settings…

When setting up molecular dynamics simulations for a series of molecular conformations, choosing the right periodic box parameters can lead to more efficient simulations and better results. In SAMSON’s GROMACS Wizard, users working with multiple conformations have two main options…

For researchers using GROMACS, setting up pulling simulations often requires creating custom index groups—say, to specify exactly which atoms or chains to pull. But writing index groups by hand in GROMACS can be awkward, especially when you’re dealing with complex…

Have you ever wanted to try out a new analysis workflow but hesitated because setting everything up from scratch seemed daunting? If you’re exploring how to predict protein-ligand complexes using NMR data, there’s a helpful shortcut in SAMSON worth knowing:…

When creating molecular animations in SAMSON, it’s common to spend time carefully orienting the scene to show a particular structure or interaction. But if you don’t explicitly control the camera during all frames, SAMSON might change the viewpoint midway as…

Creating compelling molecular animations can be surprisingly tedious, especially when presenting multi-component systems. A common challenge in structural bioinformatics and molecular modeling is illustrating how different components relate spatially in a complex supramolecular assembly. Whether it’s for teaching, a publication,…