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When Designing Molecules in 2D is the Smartest First Step

Designing new molecules in 3D can often feel overwhelming. Aligning atoms, exploring fragments, checking for clashes — it’s a lot to keep track of in three dimensions. But what if you could start your molecule design in a clean, simplified…

Unlocking New Molecular Modeling Capabilities with SAMSON Apps

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Setting up and running complex molecular simulations can often require a combination of software tools, each with distinct formats, workflows, or interfaces. For molecular modelers, this fragmentation can become a time sink—slowing down exploration and discovery. If you’ve ever thought,…

A Simpler Way to Track Molecular Simulations in the Cloud

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If you’re a molecular modeler juggling simulations across heavy-duty software like AlphaFold, GROMACS, or NVIDIA BioNeMo services, you’ve probably experienced the headaches of managing multiple jobs: locating results, checking progress, and syncing data across workstations. This can become tedious—especially if…

How to Select Terminal Residues in SAMSON with NSL

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When analyzing biomolecular structures, it’s often essential to identify and isolate terminal residues—those at the ends of polymer chains, such as the N-terminal or C-terminal amino acids in proteins. Whether you’re preparing a system for simulation, cleaning up a model,…

Why Your Ligand Path Sampling May Be Failing (and How to Fix It)

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Finding plausible ligand unbinding pathways in complex protein environments is a critical step in molecular modeling—but it can also be frustrating. Even with sophisticated tools, the system may return incomplete or biologically implausible results. One frequent pain point? The sampling…

Easier Than You Think: Adding and Removing SAMSON Extensions

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Many molecular modelers appreciate having specialized tools for specific simulations, from free energy estimation to advanced visualization techniques. But customizing your environment without wasting time or disrupting your scientific workflow can be a challenge. That’s where SAMSON Connect’s Extension Marketplace…

Facing Multiple Symmetries? Here’s How to Choose the Right One

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When working with large biological assemblies in molecular modeling, symmetry can unlock valuable speed-ups and insights. But with size comes ambiguity: large protein complexes often exhibit multiple plausible symmetry groups. If you’ve ever asked yourself “Which symmetry should I use?”,…

Why Can’t I See My Molecule? Understanding Hidden and Visible Nodes in SAMSON

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“Where did my structure go?” If you’ve ever worked on a molecular system in SAMSON and suddenly found that parts of your molecule seem to disappear or won’t respond to selection, you’re not alone. Visibility issues are a common source…

From Trajectory to Insight: Preparing Initial Conformations for Umbrella Sampling in SAMSON

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For molecular modelers seeking accurate free energy landscapes, Umbrella Sampling remains an essential technique. But before you can compute the Potential of Mean Force (PMF), the often overlooked bottleneck lies in one critical step: selecting meaningful initial conformations from your…

How to Limit the Search Space for Faster Protein Docking in SAMSON Hex

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One common challenge in molecular modeling is reducing protein docking times without compromising the quality of results. When you already have an idea of the binding site location, unconstrained searches can become unnecessary and slow. This blog post introduces a…