Author: OneAngstrom

One common challenge in preparing biomolecular systems for simulation is managing water molecules. While bulk solvent can be added systematically during solvation, crystal waters—those resolved in the original structure—often have functional roles, especially around the active site of biomolecules. Automatically…

Presenting molecular models poses a common challenge: how to add clarity and context while keeping viewers focused on the important molecular features. Whether you’re preparing a lecture, pitching a research project, or creating a tutorial, one issue comes up frequently:…

If you’ve ever tried to simulate ligand unbinding pathways from proteins, then you’ve likely faced the challenge of defining which atoms belong to the ligand — especially in systems containing cofactors, solvent molecules, or multiple ligands. Making a mistake at…

When creating molecular animations or presentations, one of the recurring challenges for modelers is capturing the motion of atoms over time. Whether you’re simulating binding events, assembly steps, or conformational changes, showcasing how atoms move is essential—and being able to…

Preparing a single protein structure for simulations is already a multi-step process. If you’ve ever had to do that with dozens or hundreds of PDB files, you’ve probably felt the pain of repetitive cleanup: removing unwanted molecules, adding missing atoms…

When working with molecular systems, the way data is visualized often makes a huge difference in understanding structure and function. A common challenge among molecular modelers is navigating the visual complexity of nanosystems without getting overwhelmed or missing crucial insights.…

In molecular modeling and simulations, it’s often essential not only to compute how particles move but also to clearly visualize the trajectory they follow. Whether you’re simulating protein-ligand interactions, assembling complex systems, or simply preparing a presentation, being able to…

When working with protein structures, it’s common to begin with asymmetric units from the Protein Data Bank (PDB). However, research and design tasks like analyzing quaternary structures, identifying protein-protein interfaces, or building full biological assemblies often require the generation of…