Author: OneAngstrom

Specifying the binding site in protein-ligand docking simulations is often one of the most critical — and error-prone — steps in preparing a reliable docking study. Whether you’re working with co-crystalized structures or docking into an apo form, identifying the…

If you’ve ever asked yourself, “Where did my node go?” while working in SAMSON, you’re not alone. Molecular modelers, especially those building complex systems with numerous nested components, often run into confusion when parts of their structure appear to be…

Anyone who has ever built or edited a molecular system knows this familiar moment: the accidental click, the undesired transformation, or the misplaced edit. In complex modeling environments like SAMSON, one changed parameter can ripple through your workflow. That feeling…

When working with complex biomolecular systems, it’s easy to feel overwhelmed by the sheer number of atoms, residues, ligands, and other structural elements. Whether you’re modeling a protein-ligand interaction or preparing a system for simulation, one key challenge is staying…

Building biologically realistic environments around membrane proteins is a regular challenge for molecular modelers. From preparing lipid bilayers to ensuring correct spatial orientation, the process often involves high manual overhead and repetitive trial and error. If you’ve ever struggled with…

For many molecular modelers, sharing their work effectively while keeping track of collaborations and maintaining a personal scientific identity is a challenge. Between papers, simulations, and cross-institutional projects, it’s difficult to both stay visible and control how and with whom…

If you’ve ever found yourself overwhelmed by layers of molecules, multiple structure files, and scattered Python scripts inside your molecular modeling environment, you’re not alone. As projects grow in complexity, so does the challenge of keeping your data manageable. That’s…

For molecular modelers performing umbrella sampling, generating initial conformations can often feel like a tedious and error-prone process. Whether you’re dealing with long trajectories or a set of predefined conformations, deciding where to extract your snapshots isn’t always straightforward. The…