Author: OneAngstrom

One common challenge when performing protein-protein docking is the high number of docking solutions that turn out to be incorrect upon detailed inspection. Especially when the potential binding site is already known, a full-sphere unconstrained search wastes time and resources,…

Modeling molecular systems often involves calculating the Potential of Mean Force (PMF) along a reaction coordinate. This can be essential for understanding binding affinities, reaction mechanisms, and free energy landscapes. However, performing a PMF analysis—especially assembling and processing multiple simulation…

When preparing molecular presentations, communicating structure and dynamics clearly can be a challenge. Static images often miss the 3D context, and manually aligning frames for a flyaround animation can be time-consuming and imprecise. Fortunately, if you’re using SAMSON, the Orbit…

Communicating the behavior and interactions of molecular systems is rarely straightforward. Whether you are preparing material for a presentation, teaching structural biology, or generating content for a paper, showing how molecules move and interact over time is a common challenge.…

Navigating large molecular systems and constantly switching between visual representations or performing repetitive cleaning tasks can be slow and unintuitive — especially when done through nested menus and buttons. If you’ve ever wished you could simply tell your modeling platform…

In molecular modeling, one common challenge is selecting specific subsets of atoms based on precise spatial or structural criteria. Whether you’re preparing a simulation, analyzing results, or designing nano-objects, you often need to identify atoms that meet certain conditions—for example,…

A common challenge in molecular modeling—especially in nanotechnology and materials science—is constructing large, periodic structures like carbon nanotubes (CNTs). These structures are often composed of repeated rings or motifs, and manually placing each unit is time-consuming and error-prone. If you’ve…

When working with protein-ligand complexes in solution, interpreting ambiguous NMR signals can be tricky. The NMR2 extension in SAMSON helps resolve these ambiguities using spatial restraints to predict complex structures. But to benefit from the algorithm, the first step—defining your…