What Is PDBj (Protein Data Bank Japan)

This section provides a quick introduction of the PDBj (Protein Data Bank Japan), which is a member organization of Worldwide PDB (wwPDB).

What Is PDBj (Protein Data Bank Japan)? - PBDj (Protein Data Bank Japan) is a member organization of Worldwide PDB (wwPDB). It supports browsing in multiple languages such as Japanese, Chinese, and Korean; SeSAW identifies functionally or evolutionarily conserved motifs by locating and annotating sequence and structural similarities, tools for bioinformaticians, and more.

PDBj is a project team operating under the Joint Usage and Research activities of the Institute for Protein Research, Osaka University. We maintain the single global PDB/BMRB/EMDB archives of macromolecular structures and provide integrated tools, in collaboration with RCSB PDB and BMRB in the USA, and PDBe in the EU. PDBj is supported by JST-NBDC and AMED-BINDS.

PDBj offers many search, deposition and viewer tools specialized in different areas such as NMR, electron microscopy, secondary structure sequence, similarity, function prediction chemical component, structure prediction, binding site surface structure, 3D structure, genome, etc.

For more information on PDBj, visit https://pdbj.org Website.

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

PDB (Protein Data Bank)

 What Is PDB (Protein Data Bank)

 What Is CRSB (Research Collaboratory for Structural Bioinformatics)

 What Is PDBe (Protein Data Bank in Europe)

What Is PDBj (Protein Data Bank Japan)

 VR molecular viewer by PDBj

 INSDC (International Nucleotide Sequence Database Collaboration)

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB