Molecular modelers often face a recurring challenge: how to efficiently manipulate complex structures and visually present key interactions or changes in molecular conformations. One common task is undocking groups of atoms or meshes from their docked positions. With SAMSON's Undock…

Molecular modeling often involves navigating the often-complex motions of proteins. Whether you’re dealing with conformational transitions or pathway analysis, defining the role of different protein atoms can make or break the accuracy and efficiency of your simulations. In SAMSON’s Protein…

Refining protein structures is a critical step in molecular modeling workflows. Strained residues or outliers in your protein backbone can lead to inaccuracies in simulations, docking studies, and other downstream analyses. This is where the Ramachandran Plot shines – it…

For molecular modelers, quickly visualizing molecules in a clear and interpretable format is a recurring challenge. Understanding the structure of SMILES (Simplified Molecular Input Line Entry System) data can often require translating complex strings into diagrams that are easier to…

Protein dynamics can be a complex and fascinating process, but visualizing changes in secondary structure over time can make studying these dynamics much easier. If you work in molecular modeling, you may often need to monitor how much of a…

If you’re a molecular modeler, you’ve likely faced the challenge of optimizing only a specific part of a molecule while keeping the remainder intact. This level of precision is crucial, for instance, when you’re studying local conformational changes or specific…

Understanding correlations and trends in molecular simulations is crucial for researchers and modelers aiming to decipher complex molecular behaviors. Often, raw data from simulations can be overwhelming, and trying to make sense of it may feel like searching for a…