ptmK: A computationally efficient toolkit for high-throughput lysine PTM modeling in proteins

Lysine residues in proteins are frequently modified posttranslationally, adding functional complexity to the proteome and playing critical roles in cellular regulation and disease. However, modeling these modifications in 3D protein structures remains challenging due to the limited availability of accessible and high-throughput computational tools. We present ptmK, a lightweight, standalone toolkit that enables rapid generation of lysine-modified protein structures with atomic precision. Without relying on complex infrastructure or external dependencies, ptmK supports more than 30 common lysine modifications and outputs all-atom structural models in PDB format (computationally generated). In addition to structure generation, ptmK also evaluates the modification likelihood of each lysine site based on solvent accessibility and proximity to functional regions. By integrating site evaluation with customizable modeling, ptmK enables scalable structural analysis and functional prioritization of lysine posttranslational modifications.