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).

MOTIVATION: Predicting protein structures with high accuracy is a critical challenge for the broad community of life sciences and industry. Despite progress made by deep neural networks like AlphaFold2, there is a need for further improvements in the quality of detailed structures, such as side-chains, along with protein backbone structures. RESULTS: Building upon the successes of AlphaFold2, the modifications we made include changing the losses of side-chain torsion angles and frame aligned point error, adding loss functions for side chain confidence and secondary structure prediction, and replacing template feature generation with a new alignment method based on conditional random fields. We also performed re-optimization by conformational space annealing using a molecular mechanics energy function which integrates the potential energies obtained from distogram and side-chain prediction. In the CASP15 blind test for single protein and domain modeling (109 domains), DeepFold ranked fourth among 132 groups with improvements in the details of the structure in terms of backbone, side-chain, and Molprobity. In terms of protein backbone accuracy, DeepFold achieved a median GDT-TS score of 88.64 compared with 85.88 of AlphaFold2. For TBM-easy/hard targets, DeepFold ranked at the top based on Z-scores for GDT-TS. This shows its practical value to the structural biology community, which demands highly accurate structures. In addition, a thorough analysis of 55 domains from 39 targets with publicly available structures indicates that DeepFold shows superior side-chain accuracy and Molprobity scores among the top-performing groups. AVAILABILITY AND IMPLEMENTATION: DeepFold tools are open-source software available at https://github.com/newtonjoo/deepfold.