Author: OneAngstrom

When working with complex biomolecular systems, understanding the structure of proteins at the residue and chain level is often essential. Whether you’re analyzing experimental data or designing molecular systems, pinpointing features such as conserved regions, mutation sites, or accessible residues…

When sharing molecular animations, it can be hard to clearly indicate when specific atoms or groups appear or disappear. Whether you’re showing a ligand binding event, a reaction intermediate forming, or toggling between two conformational states, your visual message can…

Communicating complex molecular structures often requires more than static images. Whether you’re preparing a conference presentation, teaching molecular biology, or sharing findings with collaborators, clear and compelling animations can make a big difference. One common challenge molecular modelers face is…

In molecular modeling, there are many times when one needs to edit or verify specific properties of atoms, bonds, or residues in a structure. Whether adjusting atomic coordinates, validating residue names, or changing selected node attributes, researchers often end up…

Whether you’re building synthetic materials, biopolymers, or drug-polymer conjugates, custom monomers are often the foundation of the molecular structures you want to model. A recurring challenge in molecular modeling is how to accurately define these monomers and reuse them consistently…

Following dynamic molecular events—like ligand binding or conformational changes—can be insightful, but it often comes with a common frustration: losing track of your region of interest when the scene changes throughout the animation. Molecular modelers know this pain too well.…

For many molecular modelers, the ability to rapidly identify molecules with specific features from a database is essential. Whether you’re looking for potential leads with fluorine groups for binding studies, or aiming to locate analogs containing nitrogen functionalities, the substructure…

Creating complex polymers often involves repeating monomer patterns, varied bond types, and the need for flexible editing. For many researchers and students in the molecular modeling field, building such custom polymer sequences can feel intimidating — especially when it involves…

Sometimes, even with a promising homology model, everything just looks right—until you dig into the backbone geometry. Strained or disallowed dihedral angles can hide within your structure, only to show up later in your simulations as instability or poor predictive…