In molecular modeling, it’s not uncommon to need fine-grained control over how parts of a molecule are optimized. Whether you’re modeling a protein undergoing a point mutation, refining a flexible loop while keeping the rest of the structure in place,…

If you’ve ever tried to work on several molecular modeling tasks at once, you’ll know how frustrating it can be to switch between files, copy molecular structures, or compare results side by side. Whether you’re simulating different conformations, comparing docking…

For many molecular modelers, a common frustration arises when editing a molecular system: what actually happens to the force field setup when you add or delete atoms? Will your simulation break? Will the parameters update accordingly—or will you be left…

If you’ve ever wondered how small changes to your molecule’s structure might affect its biochemical behavior—like modifying a carbon to a nitrogen or tagging on a fluorine—you’re not alone. Medicinal chemists and modelers routinely explore such modifications to improve properties…

Understanding how molecules interact along a reaction coordinate is a key step in molecular design. However, computing the Potential of Mean Force (PMF) often requires juggling multiple scripts, preparing files, and sorting out outputs that aren’t always intuitive. If you’ve…

Designing DNA nanostructures from scratch can be time-consuming. But if you’ve already built components in Cadnano, you don’t have to start over when moving into 3D modeling. Adenita, an extension for the SAMSON platform, allows you to directly import Cadnano-generated…