One of the most common challenges in molecular modeling today is generating reliable 3D structures of protein-ligand complexes when experimental data isn’t available. Whether you’re trying to evaluate a drug candidate, explore a new biomolecular interaction, or prepare input files…

For molecular modelers working with protein-ligand complexes, Nuclear Magnetic Resonance (NMR) remains a go-to experimental method when X-ray crystallography becomes impractical. However, interpreting NMR data in silico, especially ambiguous NOESY peaks involving unassigned methyls, can quickly turn computationally expensive. When…

Working on molecular simulations often means scaling up. Whether you’re modeling protein aggregation, crowded cellular environments, or simply running multiple replicas for statistical accuracy, duplicating protein structures is essential. But, if you’ve ever tried this manually, you’ve likely encountered issues…

If you work with large structural datasets, you’re probably familiar with the tedium of preparing multiple protein files—removing water molecules, deleting unnecessary ligands, fixing missing atoms—before launching simulations or docking studies. Doing this manually for dozens or even hundreds of…

When capturing and presenting molecular systems, clarity can often hinge on what is not shown—at least, not all at once. Whether you’re producing an educational video, walking through a molecular mechanism in a talk, or preparing a visual abstract, the…

In molecular modeling, clear communication is essential—especially when presenting molecular interactions in animations. A common challenge arises when trying to control when parts of a model, such as ligands or cofactors, appear during an animation. This is vital for storytelling…

Anyone who works with complex molecular systems knows the visual overload that can happen when too many labels clutter up the 3D view. Labels are essential to highlight atoms, residues, or entire molecules — but depending on your current zoom…

Anyone working with molecular dynamics simulations using GROMACS has probably encountered this issue: you’re customizing your .mdp files, loading them into a graphical interface, and — suddenly — some of your expected parameters are nowhere to be found. Frustrating? Definitely.…

Have you ever needed to illustrate a molecular mechanism that includes a clear visual spin or rotation between two states? Whether you’re preparing a presentation, teaching a concept, or documenting conformational changes between two poses, showing how a group of…