Author: OneAngstrom

Covalent docking remains a critical step in the design of irreversible enzyme inhibitors and other chemically reactive compounds—but the technical challenges involved can often outweigh the benefit, especially for those new to the field. Setting up such systems manually can…

If you’ve ever struggled with preparing a reliable set of starting structures for Umbrella Sampling in GROMACS, you’re not alone. Selecting the right initial conformations along a reaction coordinate can be tedious, especially when you’re trying to balance coverage and…

Molecular modeling is not only about computing accurate data—it’s also about communicating results clearly. Whether you’re preparing a presentation for collaborators, teaching a class, or creating a validation animation for reviewers, it’s crucial to control where your audience is looking.…

One of the most time-consuming tasks in molecular modeling is consistently producing clear and accurate representations of complex molecular systems. Switching representations, tweaking visibility, adjusting colors, labeling atoms — these repetitive steps can quickly stack up, especially when working on…

Before running molecular dynamics or publishing a protein structure, many modelers ask themselves a crucial question: Are all the residues in my protein in reasonable conformations? Even with homology modeling or refined crystallographic data, outliers in the backbone dihedral angles—φ…

When presenting complex molecular models, especially large assemblies, one common challenge molecular modelers face is visual clutter. Whether you’re showcasing interactions, functional units, or structural domains, it’s easy for your visual narrative to become overwhelming with too many overlapping components.…

Preparing ligands for docking can often slow down workflows in molecular modeling. Whether you’re running structure-based virtual screening campaigns or docking a few analogs to evaluate potential binding modes, the quality of your ligand structures directly impacts the reliability of…

When working with protein structures from the Protein Data Bank (PDB), researchers commonly analyze individual asymmetric units. However, much of the biological function and structural insight lies beyond the asymmetric unit — in the full biological assembly. These complete assemblies…

When setting up molecular dynamics simulations using GROMACS, one common but often confusing step is defining your system’s boundary conditions. Molecular modelers frequently ask: Which unit cell shape is best for my system?. This blog post explores this issue and…