Wednesday, February 28, 2018

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank

Jianjiong Gao  Andreas Prlić  Chunxiao Bi  Wolfgang F. Bluhm  Dimitris Dimitropoulos Dong Xu  Philip E. Bourne  Peter W. Rose  

 Bioinformatics, 2017,  2047–2049,
https://doi.org/10.1093/bioinformatics/btx101

We developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). Information on more than 400 types of protein modifications were collected and curated from annotations in PDB, RESID, and PSI-MOD. We divided these modifications into three categories: modified residues, attachment modifications, and cross-links. We have developed a systematic method to identify these modifications in 3D protein structures. We have integrated this package with the RCSB PDB web application and added protein modification annotations to the sequence diagram and structure display. 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.
Protein modifications mapped onto the sequence and structure of ferredoxin I (PDB ID 1GAO, Chen et al., 2002). The Protein Modification track highlights residues involved in two iron-sulfur clusters (3Fe-4S (F3S): triangles/lines and 4Fe-4S (SF4): diamonds/lines). The number of edges of the protein modification icon symbolizes the number of residues involved in the modification. The 4Fe-4S cluster is displayed in the Jmol structure window above the sequence display
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