When working with molecular models, one recurring challenge is efficiently selecting specific atoms based on their positions or properties. Whether slicing a geometry, isolating substructures, or modifying subsets of atoms, manual atom selection is often tedious and error-prone—especially in larger…

Studying molecular transitions—the steps a molecule takes between two states—is key to understanding biological processes, designing drugs, and optimizing materials. Transition path sampling and optimization methods, like the Parallel Nudged Elastic Band (P-NEB) approach in SAMSON, help researchers explore these…

Transferring data between different tools and formats is one of the most common pain points in molecular modeling workflows. Whether you’re importing a complex structure from a crystallography database, exporting atomic trajectories after a long simulation, or working with DNA…

When computing the Potential of Mean Force (PMF) in molecular simulations, there’s a crucial detail that can often be overlooked: the quality of sampling along the reaction coordinate. Poor sampling can lead to misleading energy profiles, potentially invalidating the conclusions…

One of the most common tasks molecular modelers face when preparing a simulation is cleaning up PDB structures imported from the Protein Data Bank. These files often contain crystal waters—some of which are essential for maintaining protein active sites, while…

When working on DNA nanostructures, it’s common to rely on tools like Cadnano or custom editors to design staple and scaffold strands. However, as research progresses and designs become more modular, the ability to reuse and import these components across…

When modeling complex molecular systems, selecting the right atoms is often a necessary but tedious task. Visual selection can be uncomfortable in dense structures, and name-based selection isn’t always flexible enough. But with mathematical expression-based selection, you can gain precision…

Crystallography plays a vital role in material science, nanotechnology, and structural biology. But even for experienced modelers, visualizing and interacting with crystal structures can feel abstract. A recurring challenge is analyzing how crystals look and behave along specific crystallographic planes…

One of the most common issues molecular modelers encounter during structure-based drug design is poor-quality docking results due to incorrect ligand geometries. If your ligand library includes 2D structures or molecules with unrealistic bond angles, the scoring functions used during…