If you’re a molecular modeler dealing with complex simulations, you’ve probably faced challenges in implementing pulling simulations to study inter-molecular interactions or molecular dynamics. In this blog post, we’ll dive into the concept of center-of-mass (COM) pulling, a crucial simulation…

When studying molecular systems, understanding how a structure interacts with its environment, folds, or binds to other molecules can be a persistent challenge. A useful metric to tackle this problem is the Solvent-Accessible Surface Area (SASA). Whether you are analyzing…

Visualizing molecular structures with depth and clarity is crucial for molecular modelers, but sometimes flat 2D renderings can fail to provide an intuitive sense of depth. This is where SAMSON’s Ambient Occlusion settings can make a real difference in improving…

Protein modeling often requires comparing the structures of molecules to identify conserved residues, analyze conformations, or assist in downstream applications like homology modeling. However, aligning protein structures manually can be challenging and time-consuming—especially when precise superpositions are critical. SAMSON’s Protein…

For molecular modelers, understanding protein conformations and how they evolve along a path can be challenging. A vital tool to address this problem is the Ramachandran plot, which provides a clear visualization of protein backbone torsion angles (phi and psi).…

Molecular modelers often encounter a common challenge: how can you optimize specific regions of a molecule without affecting the rest of its structure? This is especially relevant when working on large molecules where only a local part of the system…

For molecular modelers, precision at the sub-molecular level can make all the difference. Whether you’re crafting a new molecule or fine-tuning an existing one, optimizing specific parts rather than the entire structure is often critical. This is where SAMSON’s ability…

For molecular modelers, achieving precise and dynamic control over simulations has often been a challenge. SAMSON, an integrative molecular design platform, offers an innovative solution with its interactive simulation capabilities, enabling users to conduct real-time modeling while maintaining full control…