SAMSON Blog – Page 116

Quickly Generate Molecular Analogs with a Simple SMARTS Pattern

If you’re working in molecular design or drug discovery, you’ve probably come across the need to explore structural analogs of a lead compound – whether to improve binding, reduce toxicity, or evade metabolic vulnerability. Traditionally, this can require manual editing…

Filtering Residues by Charge in SAMSON: A Quick Guide for Molecular Modelers

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When dealing with biomolecular systems, especially proteins, understanding the charge distribution of residues plays a critical role in many modeling tasks. Whether you’re preparing input for electrostatics calculations, identifying potential binding sites, or simply studying protein-ligand interactions, selecting residues based…

Avoiding Solvent Clashes in Coarse-Grained Simulations with GROMACS Wizard

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When setting up molecular dynamics (MD) simulations using coarse-grained (CG) models, one recurring issue modelers face is improper solvation: water molecules overlapping with solute atoms or each other. This can happen easily when using default settings that are not tailored…

Making Molecular Components Appear on Cue in Your Animations

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When creating molecular animations, one frequent challenge is controlling when specific components appear during your presentation. Whether you’re highlighting a ligand binding to a protein or the formation of a molecular assembly, the timing of element visibility is essential to…

Clicking Your Way Through Proteins: Inspecting Residues with the Interactive Ramachandran Plot

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When working with proteins, even a single poorly-placed residue can make the difference between a stable simulation and a failed model. For molecular modelers, quickly identifying and fixing conformational outliers is more than just helpful – it’s essential. But in…

Are You Modeling the Right Bond Type?

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When working on molecular models—whether your goal is to study protein-ligand interactions, simulate quantum properties, or simply clean up your structure—getting bond types right is essential. Unfortunately, many modelers overlook this step, which can lead to subtle but significant errors…

Making Your Molecules Stand Out: A Guided Tour of SAMSON’s Rendering Preferences

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Molecular modelers often struggle with one recurring challenge: visual clarity. Whether you’re preparing figures for a publication, a presentation, or simply trying to interpret complex systems more clearly, the way molecules are rendered can have a huge impact on your…

Replaying Molecular Trajectories in Reverse: A Timesaving Trick in SAMSON

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Visualizing molecular transitions is a fundamental part of molecular modeling. Whether you’re tracking a conformational change, reviewing a reaction pathway, or simply cycling between states, being able to loop animations smoothly—and sometimes in reverse—can make a big difference. In SAMSON,…

Freeing Bound Molecules: Create Undocking Animations in SAMSON

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When modeling molecular interactions, demonstrating a ligand binding to a receptor is essential. But what about the reverse process? Undocking animations are just as important, especially when preparing presentations, educational content, or investigating energy release during the unbinding stage. In…

Never Guess Again: Measuring Distances Between Atoms in SAMSON

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Whether you’re analyzing protein-ligand interactions or checking geometry optimization results, measuring precise atomic distances is a routine—but vital—task in molecular modeling. Yet, for many users, keeping track of those measurements or quickly accessing the most relevant ones can be frustrating…