Author: OneAngstrom

When studying protein conformational changes, modeling how a protein transitions from one conformation to another is just the beginning. Molecular modelers often need to analyze and share results: extract key conformations, view transition energies, or export trajectories for visualization and…

If you’re studying protein dynamics, a common challenge is identifying conformational pathways between two known states. Before diving into complex simulations or heavy computations, one crucial step must be done right: loading and preparing your protein’s conformational models correctly. In…

Water molecules in protein structures from the Protein Data Bank (PDB) can either be essential for function or relics from crystallographic data that don’t matter for your simulation. Knowing how to selectively remove undesired water molecules while preserving those in…

When modeling conformational transitions in proteins, ensuring that the start and goal structures are properly aligned and compatible is essential. If your starting and ending conformations are not set up correctly, most path-finding algorithms will either fail or return meaningless…

In molecular simulations, especially when preparing systems using GROMACS, it’s common to remove water molecules from the initial structure to avoid unwanted interactions or duplicate solvation. However, researchers often face a recurring dilemma: how can you quickly remove unnecessary crystal…

Anyone who has worked with protein structures knows that small structural issues can lead to big problems down the road. Whether you’re docking ligands, running molecular dynamics simulations, or building models for drug screening, structure validation is what stands between…

Have you ever created a molecular visualization that felt underwhelming, despite being scientifically accurate? If your model seems flat or lacks depth, you’re not alone. One of the most common problems in molecular modeling is a lack of depth perception—making…

When visualizing molecular systems, especially during simulations or dynamic processes, it can be frustrating to lose focus on the region that truly matters. Whether it’s a ligand binding site, a protein loop in motion, or the interaction between molecular fragments,…