Molecular modelers often face the challenge of converting 2D molecular representations into 3D-ready structures for simulations, docking, and analysis. This process can be time-consuming, particularly when handling extensive SMILES datasets. Fortunately, SAMSON’s SMILES Manager, powered by RDKit, offers a streamlined…

For molecular modelers, ensuring protein structures are accurate and free from conformational strain is a crucial step before running simulations or performing analyses. One common challenge in protein modeling is identifying and correcting residues that occupy unfavorable backbone conformations. This…

Keeping a consistent viewpoint during molecular visualizations can be challenging, especially when working with large and complex simulation datasets. Imagine carefully setting up the ideal camera angle, only to lose it due to unintended movements or adjustments. For molecular modelers,…

Creating compelling molecular animations can significantly aid communication and understanding in molecular modeling. However, ensuring that your audience pays attention to critical aspects of your presentation is not always easy. This is where the Pause animation in SAMSON can make…

Cleaning up a molecular system before running simulations is a critical step for ensuring reliable results. One common issue for molecular modelers involves deciding what to do with the crystal waters found in protein structures. While some waters are essential…

Molecular modelers often need to delve deeply into the mechanics of molecular interactions to uncover potential therapeutic strategies or simply to better understand a system of interest. One challenge is studying complex protein motions, such as those of the SARS-CoV-2…

For molecular modelers, one of the most time-consuming challenges can be toggling between different perspectives of a complex molecular structure. Constantly adjusting the viewpoint to focus on specific areas or switch between wide and close-up views can disrupt workflow efficiency.…

For molecular modelers, juggling between multiple views of a structure can be a daunting task. Connecting what you see in a sequence, a structural model, and a 3D view often feels like navigating through a maze. This challenge is especially…

As a molecular modeler, you know that optimizing molecular geometries is a critical step in simulations and molecular design. Achieving stable and realistic structures is paramount, but finding the right tool for this task can be a challenge, especially when…