Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures

Abstract

Protein Data Bank Japan (PDBj, https://pdbj.org/) is the Asian hub of three-dimensional macromolecular structure data, and a founding member of the worldwide Protein Data Bank. We have accepted, processed, and distributed experimentally determined biological macromolecular structures for over two decades. Although we collaborate with RCSB PDB and BMRB in the United States, PDBe and EMDB in Europe and recently PDBc in China for our data-in activities, we have developed our own unique services and tools for searching, exploring, visualizing, and analyzing protein structures. We have also developed novel archives for computational data and raw crystal diffraction images. Recently, we introduced the Sequence Navigator Pro service to explore proteins using experimental and computational approaches, which enables experimental structural biologists to increase their insight to help them to design their experimental studies more efficiently. In addition, we also introduced a new UniProt-integrated portal to provide users with a quick overview of their target protein and it shows a recommended structure and integrates data from various internal and external resources. With these new additions, we have enhanced our service portfolio to benefit both experimental as computational structural biologists in their search to interpret protein structures, their dynamics and function.

Keywords: PDB; UniProt; data archives; protein structure; sequence analyses.