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We developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). ... By scanning all 3D structures in the PDB using BioJava-ModFinder, we identified more than 30 000 structures with protein modifications, which can be searched, browsed, and visualized on the RCSB PDB website ... Acknowledgement We thank John Garavelli for updating the RESID database and current and past RCSB PDB staff for suggestions, critical review, and testing of new features. ...doi:10.1093/bioinformatics/btx101 pmid:28334105 pmcid:PMC5870676 fatcat:7xuhkcsn5jhcrjmqakp74k4u7y