Abstract Motivation Post-translational modifications (PTMs) alter functional states and interaction specificity largely through the conformational changes they impose on protein structure. However, most existing resources remain sequence-centric and cannot reveal how chemical modifications reshape three-dimensional structures. To address this gap, we propose a structural database that systematically extracts and contextualizes modification sites within experimentally determined protein structures, providing a foundation for future studies of protein structure, function, and regulatory mechanisms. Results We present StrucPTM, a database that extracts modified residues directly from the Protein Data Bank (PDB) structures using atom-level composition rules, substantially expanding coverage beyond annotation-dependent methods. Each validated PTM modification is mapped onto a UniProt entry. The database further characterizes residues using key structural descriptors—including secondary structure, relative solvent accessibility (RSA), and whether the PTM site lies at an inter-chain interface. All chains associated with the same UniProt ID are compared and grouped into homolog sets based on sequence identity. This emphasizes structural conservation among homologs, allowing PTM-induced conformational deviations to be distinguished from unrelated sequence divergence. Availability and implementation StrucPTM offers searchable access, interactive 3D visualization, and homolog-based structural comparison through its web interface: https://prix.hanyang.ac.kr/strucptm. The source code and datasets are permanently archived on Zenodo (DOI: 10.5281/zenodo.18939125) and are accessible via GitHub (https://github.com/HanyangBISLab/StrucPTM.git). Supplementary information Supplementary data are available at Bioinformatics online.
Jeon et al. (Sat,) studied this question.