StrucPTM: a database of structurally validated protein modifications and their conformational variation

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 3D 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 interchain 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).