Molecular modelers often face a recurring challenge: selecting specific atoms out of a complex structure based on well-defined criteria such as spatial coordinates, atomic types, or custom geometrical constraints. Whether preparing a region for simulation or visualizing a portion of…

Removing water molecules may seem like a straightforward preprocessing step before running a molecular dynamics simulation. However, when dealing with experimental structures such as those from the Protein Data Bank (PDB), some of the water molecules—especially those near the active…

One of the everyday challenges in molecular modeling is building customized polymers from non-standard monomer units. Whether you’re working on conjugated systems, biomaterials, or drug-polymer conjugates, chances are you need more than a basic monomer library—you need flexibility. The Polymer…

When working on molecular systems, it’s common to revisit specific parts of a structure repeatedly: a ligand, a set of residues near the active site, water molecules, binding pockets, and more. Navigating back and forth between these selections can quickly…

In molecular modeling, where precise manipulations and iterative design are crucial, accidental changes can break a workflow—or even worse, lead to unnoticed errors in a complex system. If you’ve ever altered a molecular structure and immediately regretted it, SAMSON’s history…

One common challenge in molecular modeling is making rendered images both visually clear and scientifically appropriate. Whether you’re trying to showcase the hydrophobic pocket of a protein binding site or emphasize a drug interacting with a critical residue, the appearance…

One of the most recurring challenges faced by researchers working with coarse-grained (CG) molecular systems is system preparation. When preparing CG systems for molecular dynamics (MD) simulations using GROMACS, minor parameter misconfigurations can easily lead to inaccurate results or unstable…

If you’re working with covalent inhibitors, you probably know that setting up covalent docking studies can be tricky. From ensuring the correct chemical structure of your ligand to modifying protein residues involved in the covalent interaction, every detail impacts your…