One common challenge faced by structural biologists working with NMR-derived molecular structures is postprocessing. After initial structure generation with tools like CYANA, converting these NMR ensembles into high-quality, energy-minimized models suitable for publication or molecular design often requires manual setup…

When working with molecular trajectories, it’s often necessary to analyze not just how a system evolves forward, but also what happens when the process is reversed. For instance, in conformational studies or reaction reversibility checks, playing a path backward can…

When modeling large biological assemblies like virus capsids or multi-subunit complexes, symmetry can be a valuable asset. It helps identify repeating units, reduce simulation costs, and guide structural analysis. However, molecular modelers often encounter a common scenario: multiple symmetry groups…

If you have ever struggled to make sense of noisy Potential of Mean Force (PMF) profiles or spent hours parsing simulation folders manually, you’re not alone. For many molecular modelers, processing umbrella sampling results into clear, interpretable energy landscapes can…

Constructing carbon nanotube (CNT) models for molecular simulation or nanoengineering projects often requires carefully tuning structure-defining parameters. For many molecular modelers, this becomes a bottleneck—especially when dealing with multi-walled CNTs or trying to replicate specific geometries using external modeling tools.…

Molecular animations are powerful tools for communicating complex structural and dynamic concepts. Whether you’re presenting a conformational change, a docking event, or an interactive walkthrough of biomolecular interactions, every frame matters. But there’s a challenge many molecular modelers face: giving…

Molecular modelers often deal with complex biomolecular systems made of long sequences of residues spanning multiple chains. One common challenge is maintaining clarity when switching between views: sequences, 3D models, and structural hierarchies. SAMSON addresses this issue with the Sequence…

Working with complex molecular systems involves not just visualization, but also managing the structure of the data. For molecular modelers, this can quickly become a challenge—especially when handling large protein assemblies, predictions from AlphaFold or Chai-1, or multiple working hypotheses…

When creating molecular animations, it’s often essential to trace the movement of atoms over time. Whether you’re demonstrating a docking process, simulating molecular dynamics, or showcasing the motion generated by a custom animation, documenting the precise trajectory can be critical…