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bioRxiv · 10.64898/2025.12.21.695100

MONDE·T: A Database and Interactive Webserver for Non-Canonical Amino Acids (ncAAs) in the PDB

Waldherr, A.·Freimann, G. L.·Lupas, A. N.
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Abstract

SummaryNon-canonical amino acids (ncAAs) are understood as amino acids that are not genetically encoded. They are of wide interest for protein design and applications in pharmaceutical and cell biological research, but their impact on protein structure has not been explored systematically. We therefore collected all ncAAs in the Protein Data Bank (PDB) into the MONDE{middle dot}T database, amounting to 1,875 different chemical types in >10,000 entries. They are made accessible through a webserver that allows for data download, visualization of the structures in which they occur, plots of their backbone torsion angles compared to canonical residues, and exploration of their similarity to these. Analyses can focus on a single ncAA or a specific protein structure, illustrated here by example applications. Availability and implementationMONDE{middle dot}T is hosted at the Max Planck Institute for Biology Tu bingen, accessible online at https://mondet.tuebingen.mpg.de. The database is available for download under the Creative Commons 4.0 License.

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Waldherr, A., Freimann, G. L., Lupas, A. N.. 2025-12-23. MONDE·T: A Database and Interactive Webserver for Non-Canonical Amino Acids (ncAAs) in the PDB. https://doi.org/10.64898/2025.12.21.695100

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