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When working with protein structures, accuracy begins at preparation. One common issue molecular modelers face—especially when dealing with alternate conformations or large multimeric structures—is the need to remove unwanted chains before running simulations, conformational interpolation, or structural comparisons. For instance,…

Capturing molecular flexibility is an essential part of modern structural biology and computational modeling. Whether you’re exploring ligand accessibility, visualizing allosteric motions, or preparing morphing animations between conformations, there often comes a time when you reach an interesting molecular state…

When building or analyzing molecular structures, geometry optimization is essential to remove unrealistic geometries and prepare systems for simulations. However, classic approaches such as steepest descent can be time-consuming, especially when your structure requires large-scale structural relaxation. Fortunately, SAMSON offers…

For many molecular designers working on DNA nanostructures, a common workflow challenge lies in translating intricate 3D models into formats that are simulation-ready. This becomes especially critical when preparing systems for coarse-grained simulations like those run with oxDNA. Adenita, a…

In large protein assemblies, symmetry often plays a fundamental role in biological function and modeling workflows. However, when working with complex structures like viral capsids or multimeric proteins, automated symmetry detection tools may propose multiple symmetry groups. This can lead…

Understanding how proteins arrange themselves into larger structures is a recurring challenge in molecular modeling. Whether you’re studying quaternary structures or designing nanostructures, one issue always arises: how to easily visualize the full biological assembly from the asymmetric unit provided…

If you’ve ever run molecular dynamics (MD) simulations with GROMACS, you know how crucial the .mdp file is. It defines all the parameters that control how your simulation behaves—from minimization settings to production dynamics. But editing this file manually can…

If you’ve ever tried protein-protein docking and encountered strange results — unexpected clashes, misaligned complexes, or long computation times — chances are your system wasn’t properly prepared. Protein preparation is foundational for successful docking, yet it’s often overlooked or done…

Color is an essential tool for molecular modelers. Whether you’re communicating structural insights, visualizing properties like hydrophobicity or temperature factors, or simply enhancing the aesthetic clarity of a molecular scene, choosing the right color scheme makes a big difference. But…