OneAngstrom – Page 39

FASTA In, Structure Out: Predicting Proteins with AlphaFold-2 in SAMSON

Predicting protein structures used to be a long, resource-heavy process, often requiring local installations or complex data preparation. Today, especially with the introduction of AlphaFold-2, molecular modelers have access to powerful prediction engines remotely. However, integrating these capabilities into real…

Reducing False Positives in Protein Docking with Smart Search Domain Setup

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One common challenge in protein-protein docking is the overwhelming number of false positives generated during the search phase. These incorrect poses can significantly slow down interpretation and reduce confidence in your results. A practical strategy to minimize this issue is…

Making Molecular Trajectories Understandable with the Play Path Animation

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Communicating the subtle motion of molecular systems over time can be a challenge. Whether you’re refining a drug candidate through conformational sampling or analyzing a simulation trajectory frame by frame, one of the key difficulties for molecular modelers is presenting…

Finding the Right Groups in SAMSON Using Node Group Attributes

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When modeling complex molecular systems, quickly finding the right groups of atoms or structures becomes essential. Whether you’re analyzing secondary structures, comparing ligand sets, or managing subsets of your scene, being able to search, filter, and select groups efficiently can…

Struggling with molecular file formats? Here’s how SAMSON handles it.

OneAngstrom

One of the most frequent challenges in molecular modeling is getting your data into the software in the first place. Whether you’re working with protein structures from the Protein Data Bank, volumetric data from electron microscopy, or other simulation outputs,…

Placing Lipids Around Membrane Proteins Without Tears or Scripts

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Membrane proteins are notoriously tricky to simulate, in part because preparing a realistic environment around them can be a frustrating and time-consuming process. Modeling a lipid bilayer around a transmembrane protein usually requires specialized tools, scripting skills, and plenty of…

Want to Track How a Ligand Unbinds? Try This Simple Visualization

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One of the recurring challenges in molecular modeling is making sense of complex atomic trajectories. Whether studying how a ligand unbinds from a protein or following large-scale conformational changes, analyzing raw coordinates can quickly become overwhelming. Fortunately, there’s a straightforward…

How to Display Formal Charges Directly on Your Molecular Model

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When working with detailed molecular models, having quick access to key atomic properties can save time and boost confidence in the analysis. One such property is the formal charge of atoms – a fundamental aspect of understanding reactivity, resonance, and…

Quickly Count Specific Atom Types in Molecular Folders with NSL

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When working with complex molecular systems, it’s often necessary to select folders based on the precise number of atoms they contain. Whether you’re building datasets, analyzing molecular systems, or preparing simulations, filtering by atom counts can save time and reduce…

Avoid a Common Pitfall: Does Your System Support Molecular Modeling in SAMSON?

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Nothing’s more frustrating than downloading a sophisticated molecular modeling platform, only to realize it won’t run smoothly—or won’t even start. Whether you’re trying to analyze large protein-ligand interactions or generate molecular animations, having the right environment makes all the difference.…