Author: OneAngstrom

Designing nanotube-based nanodevices or studying their properties often means building precise atomic models, which can be a time-consuming task. If you’ve worked in nanotechnology, molecular transport modeling, or material science, you’re probably familiar with the repetitive steps needed to create…

One common challenge in molecular modeling is adapting molecular structures when atoms move during a simulation. Often, manually updating topologies like covalent bonds and atom types can slow down workflows and increase the chance of errors. If you’ve ever tried…

One common challenge when studying macromolecules is understanding and predicting how biomolecular structures open and close their active or binding sites. Whether you’re designing a drug or investigating conformational transitions, this dynamic behavior is crucial — but simulating it can…

Working with dozens (or hundreds) of PDB files can be a common challenge in computational biology and drug discovery. Whether you’re screening compounds, running molecular dynamics, or preparing datasets for machine learning, there’s one recurring issue: curating and prepping all…

When telling the story of a complex molecular system, timing and visual consistency can have a significant impact on comprehension. Many researchers and educators rely on animations to construct engaging molecular presentations. However, a common challenge arises when trying to…

Anyone who has worked with force field simulations knows that automatic atom typing and bond assignments save time—but there are times when default settings just don’t cut it. Whether you’re fine-tuning a reactive center, modeling unusual molecules, or correcting an…

Crystal structures are often taught as perfect, repetitive lattices. But in actual materials, atoms are not always perfectly placed. Defects—such as missing atoms or substitutions—can significantly change the properties of a material, from conductivity to hardness. For molecular modelers trying…

One of the common pain points in protein-protein docking is long computation times combined with a high number of false positives, especially when working with high-resolution structures. What if there were a simple strategy to significantly reduce search time and…

When preparing molecular animations, one common challenge is visual clutter. Especially in complex systems, it’s easy to lose focus on the region of interest when atoms all around are shifting, vibrating, or drifting across frames. This can be distracting and…

When creating animations of molecular systems, one of the recurring challenges is designing smooth and informative transitions between camera views. Do you ever find yourself manually adjusting the camera just to get that consistent slide across a molecule or complex…