One of the frustrating challenges in molecular modeling is understanding and simulating large conformational changes in biomolecular complexes. For researchers working on viral mechanisms or drug discovery, visualizing the conformational transition of key viral components—such as the spike glycoprotein on…

Designing complex polymers from scratch can be a rewarding yet error-prone task. A common challenge faced by molecular designers is managing repeat units (monomers) and their connections, especially when diverse bond types and large polymer chains are involved. If you’ve…

Refining protein structures can be a subtle and time-consuming process. One of the common challenges molecular modelers face is fixing residues with unfavorable conformations before running simulations. A residue that slightly deviates from a stable region in Ramachandran space can…

Creating molecular animations often involves showing or hiding specific atoms, residues, or molecular structures across time. But if you’re changing visibility in a manual, step-by-step process, it can quickly become tedious—especially if you’re trying to time these changes precisely in…

Running molecular simulations in the cloud can be an efficient way to access high-performance computing resources, but staying organized and in control of your calculations is another matter entirely. If you’ve ever struggled to manage multiple job states, find your…

When working on complex molecular models, clear and informative labeling is essential. But what happens when your scene becomes crowded, or when you zoom in and out frequently to explore different scales of your system? With SAMSON, labels can be…

Molecular modelers often generate complex trajectories—whether from structural transitions, docking analyses or dynamics—but presenting these transitions clearly can be difficult. Communicating results, sharing insights with colleagues, or documenting a simulation’s progress often demands more than static images. This is where…

Creating compelling and clear scientific visuals can be a challenge for molecular modelers. Whether you’re preparing a presentation, sharing your latest findings, or teaching students about molecular structures, you want your audience to understand the spatial arrangement of atoms—without needing…

One of the first tasks after building or importing a molecular structure is preparing it for simulation. But here’s a common dilemma faced by many molecular modelers: the geometry looks mostly correct, there are only subtle non-idealities, but running a…