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Cite the PDB archive

Please cite "the PDB archive" with the reference (31) in the list of publications.


  1. Protein Data Bank: the single global archive for 3D macromolecular structure data
    wwPDB consortium
    Nucleic Acids Research 47(D1): D520-D528 (2019) [PubMed] [doi:10.1093/nar/gky949]
  2. New tools and functions in Data-out activities at Protein Data Bank Japan (PDBj)
    Kinjo, A.R., Bekker, G.-J., Wako, H., Endo, S., Tsuchiya, Y., Sato, H., Nishi, H., Kinoshita, K., Suzuki, H., Kawabata, T., Yokochi, M., Iwata, T., Kobayashi, N., Fujiwara, T., Kurisu, G. and Nakamura, H.
    Protein Science 27 (1): 95-102 (2018) [PubMed] [doi:10.1002/pro.3273]
  3. Protein Data Bank Japan (PDBj): Updated user interfaces, Resource Description Framework, analysis tools for large structures
    Kinjo, A.R., Bekker, G.-J., Suzuki, H., Tsuchiya, Y., Kawabata, T., Ikegawa, Y., Nakamura, H.
    Nucleic Acids Research 45(D1): D282-D288 (2017) [doi:10.1093/nar/gkw962]
  4. Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank
    Wako, H., Endo, S.
    Biophys. Rev. 9: 877-893 (2017) [doi:10.1007/s12551-017-0330-2]
  5. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the Protein Data Bank (PDB) Archive
    Young, J.Y. et al.
    Structure 25: 536-545 (2017) [PubMed] [doi:10.1016/j.str.2017.01.004]
  6. Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB
    Suzuki, H., Kawabata, T., Nakamura, H.
    Bioinformatics 32 (4): 619-620 (2016) [PubMed] [doi:10.1093/bioinformatics/btv614]
  7. Molmil: a molecular viewer for the PDB and beyond
    Bekker, G.-J., Nakamura, H., Kinjo, A.R.
    Journal of Cheminformatics 8:42 (2016) [doi:10.1186/s13321-016-0155-1]
  8. HOMCOS: an update server to search and model complex 3D structures
    Kawabata, T.
    J.Struct.Funct.Gennomics 17: 83-99 (2016) [PubMed] [doi:10.1007/s10969-016-9208-y]
  9. A robust method for quantitative identification of ordered cores in an ensemble of biomolecular structures by non-linear multi-dimensional scaling using inter-atomic distance variance matrix
    Kobayashi, N. et al.
    J. Biomol. NMR 58 (1): 61-67 (2014) [PubMed] [doi:10.1007/s10858-013-9805-z]
  10. Exhaustive comparison and classification of ligand-binding surfaces in proteins.
    Murakami, Y., Kinoshita, K., Kinjo, A.R., Nakamura, H.
    Protein Science 22 (10): 1379-1391 (2013) [PubMed] [doi:10.1002/pro.2329]
  11. Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables.
    Wako, H., Endo, S.
    Comp.Biol.Chem. 44 22-30 (2013) [PubMed] [doi:10.1016/j.compbiolchem.2013.02.006]
  12. GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution
    Kinjo, A. R.; Nakamura, H.
    BIOPHYSICS 8: 79-94 (2012) [PubMed] [doi:10.2142/biophysics.8.79]
  13. Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.
    Kinjo, A.R., Suzuki, H., Yamashita, R., Ikegawa, Y., Kudou, T., Igarashi, R., Kengaku, Y., Cho, H., Standley, D.M., Nakagawa, A., Nakamura, H.
    Nucleic Acids Research 40(D1): D453-D460 (2012) [PubMed] [doi:10.1093/nar/gkr811]
  14. GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.
    Kinjo, A.R., Nakamura, H.
    BIOPHYSICS 8: 79-94 (2012) [doi:10.2142/biophysics.8.79]
  15. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database
    Kobayashi, N. et al.
    J. Biomol. NMR 53 (4): 311-320 (2012) [PubMed] [doi:10.1007/s10858-012-9641-6]
  16. Bridging the gap between single-template and fragment based protein structure modeling using Spanner
    Lis, M., Kim, T., Sarmiento, J., Kuroda, D., Dinh, H., Kinjo, A.R., Amada, K., Devadas, S., Nakamura, H., Standley, D.M. Immunome Res. 7:1–8 (2011)
  17. SeSAW: balancing sequence and structural information in protein functional mapping.
    Standley, D.M., Yamashita, R., Kinjo, A.R., Toh, H., Nakamura, H.
    Bioinformatics 26: 1258-1259(2010) [PubMed] [doi:10.1093/bioinformatics/btq116]
  18. Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study
    Kinjo, A.R., Nakamura, H.
    Journal of Molecular Biology 399: 526-540 (2010) [PubMed] [doi:10.1016/j.jmb.2010.04.028]
  19. Comprehensive structural classification of ligand-binding motifs in proteins
    Kinjo, A.R., Nakamura, H.
    Structure 17 (2): 234-246 (2009) [PubMed] [doi:10.1016/j.str.2008.11.009]
  20. Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model
    Kawabata, T.
    Biophys J 95(10): 4643-4658 (2008) [PubMed] [doi:10.1529/biophysj.108.137125]
  21. Recent developments in the MAFFT multiple sequence alignment program
    Katoh, K., Toh, H.
    Brief. Bioinform. 9 (4): 286-298 (2008) [PubMed] [doi:10.1093/bib/bbn013]
  22. ASH structure alignment package: sensitivity and selectivity in domain classification
    Standley, DM, Toh, H., Nakamura, H.
    BMC Bioinformatics 8: 116 (2007) [PubMed] [doi:10.1186/1471-2105-8-116]
  23. eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
    Kinoshita, K., Murakami, Y., Nakamura, H.
    Nucleic Acids Res. 35: W398-402 (2007) [PubMed] [doi:10.1093/nar/gkm351]
  24. Similarity search for local protein structures at atomic resolution by exploiting a database management system
    Kinjo, A.R., Nakamura, H.
    BIOPHYSICS 3: 75-84 (2007) [doi:10.2142/biophysics.3.75]
  25. KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
    Kobayashi, N. et al.
    J. Biomol. NMR 39 (1): 31-52 (2007) [PubMed] [doi:10.1007/s10858-007-9175-5]
  26. CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
    Kinjo, A.R., Nishikawa, K.
    BMC Bioinformatics 7: 401 (2006) [PubMed] [doi:10.1186/1471-2105-7-401]
  27. GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures
    Standley, D.M., Toh, H., Nakamura, H.
    BMC Bioinformatics 6: 221-239 (2005) [PubMed] [doi:10.1186/1471-2105-6-221]
  28. Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequences using critical random networks
    Kinjo, A.R., Nishikawa, K.
    BIOPHYSICS 1: 67-74 (2005) [PubMed] [doi:10.2142/biophysics.1.67]
  29. eF-site and PDBjViewer: database and viewer for protein functional sites
    Kinoshita, K., Nakamura, H.
    Bioinformatics 20 (8):1329-1330 (2004) [PubMed] [doi:10.1093/bioinformatics/bth073]
  30. ProMode: a database of normal mode analyses on protein molecules with a full-atom model
    Wako, H., Kato, M., Endo, S.
    Bioinformatics 20 (13):2035-2043 (2004) [PubMed] [doi:10.1093/bioinformatics/bth197]
  31. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
    Kinoshita, K., Nakamura, H.
    Protein Science 12 (8): 1589-1595 (2003) [PubMed] [doi:10.1110/ps.0368703]

Cite a PDB structure entry

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  • An entry with a published primary citation(PDB ID and primary citation)

    PDB ID: 102L
    D.W. Heinz, W.A. Baase, F.W. Dahlquist, B.W. Matthews (1993) How Amino-Acid Insertions are Allowed in an Alpha-Helix of T4 Lysozyme Nature 361:561.

  • An entry without a published primary citation(PDB ID, author names, and title)

    PDB ID: 1CI0
    W. Shi, D.A. Ostrov, S.E. Gerchman, V. Graziano, H. Kycia, B. Studier, S.C. Almo, S.K. Burley, New York Structural GenomiX Research Consortium (NYSGXRC). The Structure of PNP Oxidase from S. cerevisiae

  • An entry may also be referenced using its Digital Object Identifier (DOI).

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    e.g.) 10.2210/pdb4hhb/pdb
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Created: 2018-05-15 (last edited: 4 weeks ago)2020-10-30
PDB entries from 2020-11-18