When working on multi-component molecular systems—such as protein-ligand complexes, nanostructures, or assembling ligand libraries—being able to precisely align and position structures is essential. But manual alignment can be both time-consuming and error-prone, especially when scaling operations or ensuring consistency across…

One of the recurring challenges in protein modeling is ensuring that your structure is biologically plausible before advancing to simulations. Even after refinement steps, it’s not uncommon to stumble upon strained residues — local backbone conformations that fall outside allowed…

Running molecular dynamics (MD) simulations is only half the work—the other half is interpreting and importing your results correctly. Many molecular modelers face the recurring challenge of efficiently handling large MD simulation data, especially with regards to choosing what to…

If you’re working in a collaborative environment or switching between devices, you’ve probably run into this issue: how to share and access molecular models across machines without losing files or struggling with mismatched folders. In molecular modeling, that friction can…

When working with complex molecular systems, especially when comparing molecular structures, preparing input for simulations, or visualizing assemblies, it’s important to have your structures neatly positioned and consistently oriented. Yet too often, molecular modelers find themselves manually adjusting atoms and…

If you’ve ever spent too long trying to create a smooth molecular docking animation—manually adjusting atomic positions or writing complex scripts—you’re not alone. Visualizing docking movements between molecules or between a ligand and a receptor can be time-consuming, especially when…

One common challenge in molecular simulations is determining whether you’ve sampled enough along the reaction coordinate during umbrella sampling. Incomplete coverage can lead to artifacts in the computed free energy profiles, making them unreliable. If you’ve ever spent days running…

Have you ever zoomed into your molecular system in SAMSON and wondered where your carefully added labels went? Or perhaps you stepped back from a large complex and the labels cluttered the view? If you work with molecular models and…