Author: OneAngstrom

When modeling protein-ligand complexes from NMR data, one of the trickiest steps is translating NOESY cross-peaks into distance restraints that can be used for structure prediction. In particular, if you’re using NMR2 in SAMSON to interpret methyl-based NOESY data, you’ll…

When investigating molecular recognition, drug binding, or unbinding mechanisms, tracking how a ligand moves through a protein is crucial. However, manually extracting these trajectories into formats suitable for downstream analysis or visualization can be both tedious and time-consuming. If you’ve…

When preparing molecular dynamics simulations in GROMACS, many modelers use gmx make_ndx to create custom index groups. You might want to separate domains, pull particular atoms, or track specific regions of a protein. However, repeating the same selection operations for…

For molecular modelers working in institutional settings—especially students and researchers without administrative privileges on their workstations—software installation can be a persistent challenge. Many powerful scientific tools require admin rights, which slows down onboarding and introduces a frustrating dependency on IT…

If you’ve ever tried to model glycosylated proteins, you know how quickly the visual landscape becomes crowded. When it comes to the SARS-CoV-2 spike protein, which mediates viral entry into human cells, the challenge is even greater: the spike is…

For molecular modelers working across different machines or collaborating remotely, keeping track of simulation jobs—especially cloud-based ones—can quickly become a challenge. Whether you’re predicting protein structures with AlphaFold or running dynamics using GROMACS, losing oversight of your running jobs, outputs,…

For many molecular modelers, visual clutter and unclear structural representations slow down analysis and discovery. Colors that aren’t well chosen can obscure rather than reveal important differences in structures—such as charge distributions, chain boundaries, or hydrophobic patterns. That’s where fine-grained…

Visualizing molecular interactions is key to understanding complex biological processes, especially when communicating with collaborators or during presentations. Molecular modelers often need to show how a ligand undocks from a receptor to highlight binding interactions, conformational changes, or docking reversibility.…

When creating molecular presentations or studying molecular interactions, conveying motion effectively is often a key challenge. Molecular modelers may struggle to emphasize subtle structural dynamics or make their models feel more alive during presentations. If you’ve ever had a hard…