If you’ve ever opened a complex biomolecular structure only to be overwhelmed by a tangle of atoms and bonds, you’re not alone. Structural biologists, computational chemists, and anyone working with molecular systems often face the challenge of understanding 3D molecular…

When working with large molecular systems, navigating and managing multiple areas of interest—like ligands, active sites, water molecules, or flexible loops—can quickly become overwhelming. Re-selecting nodes every time you want to zoom in on a specific section or perform operations…

One common source of frustration in molecular simulations is manually managing and entering the right files at each step in your workflow. If you’ve ever tried to launch an Energy Minimization step in GROMACS and struggled with locating the correct…

Molecular modeling often involves juggling multiple windows, constant tool switching, and keeping track of complex structural changes. If you’ve ever found yourself lost in a sea of panels, trying to remember where that one useful widget went—this blog post is…

For many molecular modelers, running large-scale simulations locally can be a bottleneck in their workflow. Hardware limitations, long execution times, and system configuration issues often hinder productivity. If you’ve faced such obstacles when running GROMACS simulations, SAMSON’s GROMACS Wizard offers…

Building lipid layers around membrane proteins is a routine yet tedious task in molecular modeling. Ensuring correct orientation and placement, preventing atomic clashes, and avoiding manual repetition are often time-consuming steps. Fortunately, SAMSON’s Molecular Box Builder provides an efficient way…

When working with large biomolecular structures, navigating through multiple chains and understanding their sequences in detail can quickly become overwhelming. Whether you’re inspecting interface residues or preparing a system for simulation, having a fast and intuitive way to examine individual…

Selecting the correct receptor is a foundational step in setting up a reliable docking simulation. Whether you are running a non-covalent or covalent docking study, errors made during this stage can severely impact your results. Yet, this step is often…

When analyzing molecular mechanisms, understanding how a system transitions between two conformations is often just as important as knowing the endpoint structures. But finding realistic, physically meaningful paths between such conformations can be a significant challenge. Molecular modelers face this…