Ptmk: A Lightweight Toolkit for High-Throughput Generation and Evaluation of Lysine Modifications in Protein Structures

Abstract

Lysine residues in proteins are frequently modified post-translationally, adding functional complexity to the proteome and playing critical roles in cellular regulation and disease. However, modeling these modifications in 3D protein structures remains difficult due to the lack of accessible and high-throughput computational tools. We introduce ptmk, a lightweight and standalone toolkit for generating lysine-modified protein structures with high speed and precision. Without relying on complex infrastructure or external dependencies, ptmk supports over 30 common lysine modifications and produces atomically resolved structural models. In addition to structure generation, ptmk evaluates the likelihood of modification at each lysine site based on spatial accessibility and proximity to functional regions. by integrating modification assessment with fast and customizable modeling, ptmk enables systematic exploration of lysine post-translational modifications across diverse protein targets. This approach provides a practical and scalable solution for probing the structural and functional consequences of lysine modifications in structural biology and protein engineering.

Keywords: PTMs, modification probabilities, lysine residues, protein structures