Author: OneAngstrom

As a molecular modeler, you want to keep your eyes on the details that matter the most, even as systems are in motion. Whether it’s tracking a ligand interacting with its binding site or observing a dynamic process within a…

Molecular modelers often face the challenge of efficiently optimizing transition paths between two states of a system. These paths are crucial for understanding molecular mechanisms, such as ligand binding or unbinding, conformational changes, and catalytic processes. However, generating a realistic…

When creating molecular presentations, one common challenge is effectively highlighting changes or dynamics in a visually intuitive way. If you’re looking to gradually hide certain atoms or bonds in your molecular model for better storytelling or targeted presentation, the Conceal…

Molecular modelers frequently encounter challenges when preparing and optimizing complex systems for accurate protein-ligand docking. Time-consuming preparation steps, such as cleaning up structural files, optimizing ligand geometry, and setting up flexible docking workflows, can be a bottleneck in the design…

Running production molecular dynamics (MD) simulations can be an intimidating step for molecular modelers, particularly when it comes to ensuring that all input structures and files are correctly prepared. If you’ve ever been at a standstill because of incomplete input…

One of the recurring challenges in molecular modeling is the tedious process of creating structured molecular environments, such as solvent boxes, lipid layers, or other molecular assemblies. These are essential for preparing realistic simulation systems, but generating them from scratch…

Molecular modelers face numerous challenges when visualizing complex molecular systems. Whether showcasing a protein-ligand interaction, preparing a presentation, or simply analyzing key structural elements, much time can be wasted manually applying individual visualization settings. This post offers a solution: visual…

If you’ve ever struggled with defining the correct sampling region for ligand unbinding pathways, you are not alone. A properly defined sampling box is critical for ensuring accurate and meaningful results in studies involving molecular dynamics and ligand path finding.…

For molecular modelers, mapping ligand-pathway simulations can often be a challenge, especially when defining the ligand and its interactions precisely within a system. The Ligand Path Finder in SAMSON offers a simple way to compute ligand unbinding pathways from a…