When simulating molecular systems, researchers often need to model multiple copies—or replicas—of the same protein. This is especially relevant for studying concentration effects, protein aggregation, or large-scale interactions. But generating coarse-grained (CG) models for these replicas can become a tedious…
When studying molecular dynamics (MD) simulations of protein-ligand complexes, one common challenge is interpreting how a ligand moves during a binding or unbinding event. Especially in crowded systems or long trajectories, it can be hard to get a clear picture…
When designing new molecules through analogue generation, one of the key challenges is identifying where to modify your existing structure in a systematic and meaningful way. Whether you’re exploring structure-activity relationships or trying to improve target binding, specifying the right…
One of the most common frustrations among molecular modelers is spending time repeatedly adjusting visualization settings to highlight the same structural regions—receptors, ligands, water molecules—across different molecular systems. Color schemes, visual styles, atom selections… it can all become time-consuming and…
When working with complex molecular models, one common challenge is efficiently identifying and isolating specific parts of the molecular structure. For protein modeling, in particular, side chains can play critical roles in interactions, conformations, and active sites. If you’re tired…
Minimizing the energy of your protein structure is a key prerequisite for accurate conformational path planning — yet it’s commonly overlooked or misunderstood. Whether you’re visualizing transitions between functional states or exploring conformational flexibility, starting from a minimized structure can…
When comparing proteins across species or mutations, understanding the conserved and variable regions can be critical for tasks like predicting functional sites, studying evolution, or preparing templates for homology modeling. However, managing both sequence and structural alignments can be unwieldy,…
For molecular modelers, one of the first and most crucial steps in any workflow is importing data. Whether you’re working with crystal structures, electron densities, or simulation outputs, starting off with the correct file format is essential. But what happens…
When modeling nanoscale systems, one recurring challenge is replicating molecular units along a specific direction with precision. Whether building DNA-inspired nanostructures, polymer chains, or carbon nanotubes, manually duplicating and aligning units is both time-consuming and error-prone. The Linear Pattern Editor…
Understanding ligand unbinding pathways can be a complex process, but once you’ve spent time simulating this motion with SAMSON’s Ligand Path Finder, the next step is often just as important: exporting the results. If you’re a molecular modeler trying to…
