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

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Lysine posttranslational modifications (PTMs) are crucial for proteome complexity, cellular regulation, and disease.
• Accurate 3D structural modeling of these PTMs is computationally challenging due to limited accessible tools.

Purpose of the Study:

• To present ptmK, a lightweight, standalone toolkit for rapid, atomic-level generation of lysine-modified protein structures.
• To enable scalable structural analysis and functional prioritization of lysine PTMs.

Main Methods:

• ptmK supports over 30 common lysine modifications.
• Generates all-atom structural models in PDB format without complex infrastructure.
• Evaluates lysine site modification likelihood based on solvent accessibility and functional region proximity.

Main Results:

• ptmK enables rapid and precise generation of computationally modeled protein structures with lysine modifications.
• The toolkit integrates structure generation with site-specific modification likelihood evaluation.
• Facilitates analysis of PTMs across diverse protein contexts.

Conclusions:

• ptmK provides an accessible and efficient solution for modeling lysine PTMs.
• The toolkit empowers researchers to perform scalable structural analysis and prioritize functional studies of PTMs.
• Enhances understanding of protein function and disease mechanisms driven by lysine modifications.