SAMSON Blog – Page 385

Filtering Molecular Backbones by Atom Count in SAMSON

When studying large molecular systems, zooming in on relevant structural groups is essential. Whether you’re analyzing protein backbones, coarse-grained models, or complex supramolecular assemblies, being able to filter groups of atoms based on structural attributes saves considerable time and helps…

How to Limit the Protein Docking Search Space in Hex

OneAngstrom

If you’ve ever performed protein-protein docking using tools like Hex, you’ve probably encountered this common challenge: docking takes time, especially when the search space is large and the receptor and ligand can explore orientations across the full 360° sphere. While…

A straightforward way to export ligand trajectories from SAMSON

OneAngstrom

If you’ve ever needed to extract the trajectory of a ligand along an unbinding path for further analysis, you’re not alone. For molecular modelers working on free energy calculations, reaction coordinate generation, or enhanced sampling setups, being able to export…

Why Understanding Node Types in SAMSON Can Save You Hours

OneAngstrom

If you’ve ever found yourself buried under a complex molecular system and unsure how to efficiently interact with its components in SAMSON, the answer might lie in understanding Node Types. Mastering node types is key to organizing, manipulating, and visualizing…

Filtering Structures by Atom Count in SAMSON’s NSL

OneAngstrom

When working with complex molecular assemblies, one of the key challenges for computational chemists and molecular modelers is filtering out irrelevant parts of a structure to focus only on regions of interest. You might be looking at thousands of components…

Switching Selections Fast When Modeling Molecules

OneAngstrom

When working with complex molecular systems, switching between different parts of a model—like a ligand, a protein pocket, or solvent shell—can quickly become tedious. Imagine selecting a group of atoms, navigating to another component, and then needing to go back…

From Conformations to Clearer Pathways: A Quick Optimization Strategy

OneAngstrom

When modeling molecular systems, capturing the transition between two known structures—say, a ligand binding or unbinding event—often involves generating intermediate conformations. Although these conformations may be linearly interpolated or derived using dedicated algorithms like the Ligand Path Finder, they rarely…

Smooth Molecular Trajectories Without Scripting: A Close Look at the ‘Play path’ Animation

OneAngstrom

One of the frequent challenges in molecular modeling is presenting trajectories in a way that conveys structural changes clearly and seamlessly. Whether you’re cycling through conformations, visualizing motion along a reaction coordinate, or showing docking sequences, creating a smooth and…

Building Lipid Layers Around Proteins Without the Headache

OneAngstrom

Setting up simulations of membrane proteins often starts with a significant bottleneck: building a reliable lipid layer around a protein. This step is critical for many molecular modeling projects, from studying membrane protein dynamics to simulating lipid-mediated interactions. Yet, the…

From SMILES to 3D Structures in Seconds: A Practical Guide for Molecular Modelers

OneAngstrom

For many molecular modelers, preparing accurate 3D structures from lists of SMILES codes can become a repetitive and tiresome step. Whether you’re building a compound library, exploring analogs, or preparing systems for simulations, having a fast, reliable way to convert…