The most recent paper on BioJava was written in February 2017. This paper detailed a new tool named BioJava-ModFinder. This tool can be used for identification and subsequent mapping of protein modifications to 3D in the Protein Data Bank (PBD). The package was also integrated with the RCSB PDB web application and added protein modification annotations to the sequence diagram and structure display. More than 30,000 structures with protein modifications were identified by using BioJava-ModFinder and can be found on the RCSB PDB website.