Author: OneAngstrom

When working with molecular modeling, force fields like the Universal Force Field (UFF) can automatically determine atom types, bonds, and bond orders based on molecular geometry. While this is convenient, it can sometimes lead to frustrating mismatches if the automatic…

One common challenge in molecular modeling is distinguishing molecular features in dense or complex structures. When visualizing intricate biomolecular environments, depth perception becomes crucial to avoid misinterpretation — especially when analyzing binding interfaces, cavities, or packed atom regions. That’s where…

One of the challenges molecular modelers often face is the lack of real-time feedback when manipulating structures. Whether you’re refining a structure, adjusting a geometry, or exploring potential distortions, waiting for a full simulation step—or hitting “run” dozens of times—can…

When working with homologous proteins from different organisms or mutant variants, automated structural alignment tools are helpful—but often, they align the entire structure. This can be problematic if you’re interested in comparing specific regions only, like a conserved binding pocket…

If you’ve ever tried to model carbon nanotubes (CNTs), you’ve probably run into the challenge of selecting the right n and m parameters. These parameters define the chirality and radius of a CNT—fundamental structural elements that impact its electronic and…

Molecular modelers working with large biological systems like viral spike proteins often face the challenge of understanding conformational motions — especially when experimental data is limited to static states. This becomes particularly important for studying viral entry mechanisms, such as…

Collaboration is a central part of the molecular modeling workflow. Whether working across research teams, departments, or institutions, scientists often need to exchange complex molecular data. However, molecular structure files can come with numerous dependencies, metadata, and large associated datasets.…

Visualizing molecular trajectories is essential for understanding complex behaviors such as conformational changes, docking events, or transitions between molecular states. But synchronizing multiple paths or smoothly animating a recorded trajectory can be challenging—especially when the number of frames doesn’t match…

Integrating complex tools is often a roadblock for molecular modelers. Whether it’s accessing external software, running simulations, or visualizing structure-function relationships, the ecosystem can feel fragmented. You’re forced to juggle between environments — installing plugins, converting file formats, or writing…

Before running molecular simulations or refining homology models, it’s important to ensure your structure is sound. One common problem? Backbone conformations that fall into disallowed regions of a Ramachandran plot. These typically indicate strained residues, which can affect the stability…