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…

Have you ever struggled to clearly communicate a molecular mechanism or structural change during a presentation or video? For molecular modelers and educators, timing when parts of a molecule appear or disappear can make the difference between confusion and clarity.…

When using SAMSON for molecular modeling, integrating powerful Python packages can significantly improve your workflow, especially if you’re automating simulations, analyzing data, or integrating machine learning into your research. However, choosing the right environment and knowing how to manage Python…

Designing DNA nanostructures is just the beginning. For researchers working in structural DNA nanotechnology, the ability to export a design for further simulation is a critical step in the workflow. Whether you’re preparing input for coarse-grained simulation using oxDNA or…