A Simpler Way to Run AlphaFold-2 with SAMSON

Predicting the 3D structure of proteins used to require extensive computational setups and technical expertise. For many molecular modelers, integrating AlphaFold-2 into their workflow means either accessing a command-line toolchain or relying on third-party web services — both of which…

From Click to Tube: Building Carbon Nanotubes with Your Mouse

Creating realistic models of nanostructures like carbon nanotubes (CNTs) can be time-consuming and technically complex. For molecular modelers and materials scientists, the ability to rapidly generate customizable CNTs is often crucial for prototyping device components, performing simulations, or illustrating theoretical…

Fade Away: A Simple Technique to Transition Molecular Visibility

Struggling with presenting complex molecular scenes in a clean, digestible way? If you often build animations to showcase conformational changes, protein-ligand interactions, or intricate visualizations involving multiple overlapping layers, you’ve probably asked yourself: How do I control what’s visible and…

Building Smooth Molecular Animations with Keyframes in SAMSON

Creating scientific animations of molecular systems can be time-consuming, and even experienced modelers sometimes face challenges with accurately communicating dynamic behaviors. One common pain point many encounter is smoothly moving atoms or molecular fragments across frames without introducing artifacts or…

When (and Why) You Should Minimize Ligands Before Docking

Preparing ligands for docking can feel like a minor step, especially when your molecular modeling workflow is already complex. But overlooking ligand minimization can lead to misleading docking results and longer computation times. In this blog post, we’ll walk through…