Author: OneAngstrom

When preparing a molecular dynamics simulation involving pulling—such as center-of-mass (COM) pulling—one of the most overlooked yet critical steps is correctly defining the simulation box size. A common pitfall for modelers is encountering artifacts due to improper box dimensions, especially…

One of the most common questions molecular modelers have when setting up docking experiments is: “Where should I define the search space?” Whether you’re targeting a known binding pocket or screening broadly across the protein, defining the search domain correctly…

Presenting complex molecular models can be a challenge when important parts of the structure overlap or obscure one another. Whether you’re preparing a presentation, recording a molecular animation, or just trying to better understand your system, being able to temporarily…

When preparing molecular animations for presentations or scientific communication, molecular modelers often face a recurring challenge: how to present the structure dynamically without altering its real position? Sometimes, rotating or moving the molecule can be misleading or distracting—especially when showing…

Going from a list of SMILES strings to functional 3D molecular structures can still feel like a chore, especially when you need to process multiple molecules quickly and visualize them in appropriate software. If you’re working in drug discovery, molecular…

Accurately comparing proteins is a cornerstone of molecular modeling, whether you’re examining point mutations, comparing homologs across species, or preparing a structure for homology modeling. But when working with multi-chain proteins or oligomeric complexes, sequence alignment at the chain level…

Managing tools in a molecular modeling platform can often be time-consuming. Whether you’re trying to test a new analysis method or need to streamline your modeling interface, the ability to easily add or remove functionality matters. In SAMSON, these tools…

One of the recurring challenges in molecular modeling is that integrating external tools and scripts often disrupts your workflow. Whether you rely on docking programs, simulation pipelines, or visualization utilities, switching between environments—coupled with writing tedious wrapper code—can slow down…