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…

Creating realistic animations of conformational changes in biomolecules often feels like a daunting challenge. Full molecular dynamics (MD) simulations can take days or even weeks to run, and demand high-performance computing resources. But what if you simply want to visually…

In molecular modeling, a common challenge is consistently generating clear, informative visualizations—especially when dealing with complex systems such as protein-ligand complexes, solvated structures, or multi-chain systems. Adjusting representations, selecting relevant atoms or molecules, setting color schemes, and choosing visualization models…

When preparing molecular animations—whether for a presentation, publication, or educational video—timing is crucial. A brief pause at just the right moment can give your audience the time to absorb complex molecular conformations, understand a transition, or appreciate a molecular interaction.…

For many molecular modelers, juggling multiple molecular systems during a modeling session is the norm, not the exception. Whether you’re comparing ligand binding modes, transferring fragments between structures, or running simulations on several conformations, managing multiple files effectively can be…