PDBjの引用・利用規約

PDBjの引用文献

PDBj自体を引用される場合は、文献リストの (60) (62) (69) をご利用ください。

PDBjサービスの引用文献

PDBjの各サービスを引用される場合は、以下の文献をご利用ください。文献の記載がない場合は、各サービスのURLを引用してください。

PDBエントリーの引用について

各PDBエントリーを引用する際の表記例を以下に記します。

対応するPrimary citation（引用文献）があるPDBエントリー

PDB IDで参照し、対応するDOIと引用文献の両方を使って引用してください。

PDB ID

1ema

DOI引用

Ormo, M., Remington, S.J. (1996) Green fluorescent protein from Aequorea victoria doi: 10.2210/pdb1ema/pdb

文献情報

Ormo, M., Cubitt, A.B., Kallio, K., Gross, L.A., Tsien, R.Y., Remington, S.J. (1996) Crystal structure of the Aequorea victoria green fluorescent protein Science 273: 1392-1395 doi: 10.1126/science.273.5280.1392

対応する引用文献がないPDBエントリー

PDB IDで参照し、DOI情報（エントリー著者、登録年、構造タイトル、DOI）を使って引用してください。

PDB ID

1ci0

DOI引用

Shi, W., Ostrov, D.A., Gerchman, S.E., Graziano, V., Kycia, H., Studier, B., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC) (1999) PNP Oxidase from Saccharomyces cerevisiae doi: 10.2210/pdb1ci0/pdb

PDBアーカイブの引用文献

PDBアーカイブを引用される場合は、文献リストの (31) をご利用ください。

英語文献一覧

1. • Protein Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.
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   • Protein Science
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   • e70052
   • February 19
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2. • PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.
   • Choudhary P, Feng Z, Berrisford J, Chao H, Ikegawa Y, Peisach E, Piehl DW, Smith J, Tanweer A, Varadi M, Westbrook JD, Young JY, Patwardhan A, Morris KL, Hoch JC, Kurisu G, Velankar S, Burley SK
   • Database (Oxford)
   • 2024
   • baae041
   • May 27
   • 2024
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3. • IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.
   • Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A.
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4. • Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.
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   • Structure
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   • March 14
   • 2024
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   • 10.1016/j.str.2024.02.011
5. • Community recommendations on cryoEM data archiving and validation.
   • Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S
   • IUCrJ
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6. • EMDB-the Electron Microscopy Data Bank.
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7. • Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership.
   • Xu W, Velankar S, Patwardhan A, Hoch JC, Burley SK, Kurisu G
   • Acta Crystallogr D Struct Biol
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   • 792-795
   • Sep 1
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   • 10.1107/S2059798323006381
8. • ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.
   • Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD
   • J Mol Biol.
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   • 2023
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   • 10.1016/j.jmb.2023.168021
9. • Biological Magnetic Resonance Data Bank.
   • Hoch JC, Baskaran K, Burr H, Chin J, Eghbalnia HR, Fujiwara T, Gryk MR, Iwata T, Kojima C, Kurisu G, Maziuk D, Miyanoiri Y, Wedell JR, Wilburn C, Yao H, Yokochi M
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10. • Fifty years of Protein Data Bank in the Journal of Biochemistry.
    • Genji Kurisu
    • The Journal of Biochemistry
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    • 1233-1238
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11. • Forty years of the structure of plant-type ferredoxin.
    • Genji Kurisu, Tomitake Tsukihara
    • The Journal of Biochemistry
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    • 19-21
    • 2022
    • 10.1093/jb/mvab113
12. • Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.
    • Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudou, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu
    • Protein Science
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    • 173-186
    • 2022
    • 10.1002/pro.4211
13. • History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics.
    • Kurisu G, Bekker GJ, Nakagawa A
    • Biophys Rev.
    • 14
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    • 1233-1238
    • Dec 9
    • 2022
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14. • PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.
    • Westbrook JD, Young JY, Shao C, Feng Z, Guranovic V, Lawson CL, Vallat B, Adams PD, Berrisford JM, Bricogne G, Diederichs K, Joosten RP, Keller P, Moriarty NW, Sobolev OV, Velankar S, Vonrhein C, Waterman DG, Kurisu G, Berman HM, Burley SK, Peisach E
    • J Mol Biol.
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    • 10.1016/j.jmb.2022.167599
15. • Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.
    • Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudou, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu
    • Protein Science
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    • 173–186
    • 2022
    • 34664328
    • 10.1002/pro.4211
16. • Enhanced validation of small-molecule ligands and carbohydrates in the protein databank.
    • Zukang Feng, John D.Westbrook, Raul Sala, Oliver S.Smart, Gérard Bricogne, Masaaki Matsubara, Issaku Yamada, Shinichiro Tsuchiya, Kiyoko F.Aoki-Kinoshita, Jeffrey C.Hoch, Genji Kurisu, Sameer Velankar, Stephen K.Burley, Jasmine Y.Young
    • Structure
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    • 1-8
    • 2021
    • 10.1016/j.str.2021.02.004
17. • Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.
    • Chenghua Shao, Zukang Feng, John D Westbrook, Ezra Peisach, John Berrisford, Yasuyo Ikegawa, Genji Kurisu, Sameer Velankar, Stephen K Burley, Jasmine Y Young
    • Glycobiology
    • 31
    • 9
    • 1204-1218
    • Sep 20
    • 2021
    • 33978738
    • 10.1093/glycob/cwab039
18. • The Protein Data Bank Archive.
    • Sameer Velankar, Stephen K Burley, Genji Kurisu, Jeffrey C Hoch, John L Markley
    • Methods in molecular biology
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    • 3-21
    • 2021
    • 33950382
    • 10.1007/978-1-0716-1406-8_1
19. • The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations.
    • Gert-Jan Bekker, Takeshi Kawabata, Genji Kurisu
    • Biophysical Reviews
    • 12
    • 371-375
    • 2020
    • 32026396
    • 10.1007/s12551-020-00632-5
20. • BioMagResBank (BMRB) as a Resource for Structural Biology.
    • Pedro R. Romero, Naohiro Kobayashi, Jonathan R. Wedell, Kumaran Baskaran, Takeshi Iwata, Masashi Yokochi, Dimitri Maziuk, Hongyang Yao, Toshimichi Fujiwara, Genji Kurusu, Eldon L. Ulrich, Jeffrey C. Hoch, John L. Markley
    • Structural Bioinformatics. Methods in Molecular Biology
    • 2112
    • 187-218
    • 2020
21. • Protein Data Bank: the single global archive for 3D macromolecular structure data.
    • wwPDB consortium
    • Nucleic Acids Research
    • 47
    • D1
    • D520-D528
    • 2019
    • 30357364
    • 10.1093/nar/gky949
22. • 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
    • 28815765
    • 10.1002/pro.3273
23. • Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
    • Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK.
    • Database
    • 2018
    • bay002
    • 2018
    • 29688351
    • 10.1093/database/bay002
24. • 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
    • 10.1093/nar/gkw962
25. • Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank.
    • Wako, H., Endo, S.
    • Biophys. Rev.
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    • 877-893
    • 2017
    • 10.1007/s12551-017-0330-2
26. • 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
    • 28190782
    • 10.1016/j.str.2017.01.004
27. • Validation of Structures in the Protein Data Bank.
    • Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ.
    • Structure
    • 25
    • 1916-1927
    • 2017
    • 29174494
    • 10.1016/j.str.2017.10.009
28. • 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
    • 26508754
    • 10.1093/bioinformatics/btv614
29. • Molmil: a molecular viewer for the PDB and beyond.
    • Bekker, G.-J., Nakamura, H., Kinjo, A.R.
    • Journal of Cheminformatics
    • 8
    • 42
    • 2016
    • 10.1186/s13321-016-0155-1
30. • HOMCOS: an update server to search and model complex 3D structures.
    • Kawabata, T.
    • J.Struct.Funct.Gennomics
    • 17
    • 83-99
    • 2016
    • 24384868
    • 10.1007/s10969-016-9208-y
31. • A novel loss-of-function mutation of GATA3 (p.R299Q) in a Japanese family with Hypoparathyroidism, Deafness, and Renal Dysplasia (HDR) syndrome.
    • Okawa, T., Yoshida, M., Usui, T., Kudou, T., Iwasaki, Y., Fukuoka, K., Takahashi, N., Uehara, Y., Oiso, Y.
    • BMC Endocrine Disorders
    • 15
    • 66
    • 2015
    • 10.1186/s12902-015-0065-7
32. • The Protein Data Bank archive as an open data resource.
    • Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.
    • Journal of Computer-Aided Molecular Design
    • 28
    • 10
    • 1009-1014
    • 2014
    • 10.1007/s10822-014-9770-y
33. • 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
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    • 61-67
    • 2014
    • 24384868
    • 10.1007/s10858-013-9805-z
34. • 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
    • 23934772
    • 10.1002/pro.2329
35. • 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.
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    • 22-30
    • 2013
    • 23537565
    • 10.1016/j.compbiolchem.2013.02.006
36. • How Community Has Shaped the Protein Data Bank.
    • Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.
    • Structure
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    • 1485-1491
    • 2013
    • 10.1016/j.str.2013.07.010
37. • Functional structural motifs for protein-ligand, protein-protein and protein-nucleic acid interactions and their connection to supersecondary structures.
    • Kinjo, A.R., Nakamura, H.
    • Methods in Molecular Biology
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    • 295-315
    • 2013
    • 22987360
    • 10.1007/978-1-62703-065-6_18
38. • GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.
    • Kinjo, A. R.; Nakamura, H.
    • Biophysics
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    • 79-94
    • 2012
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    • 10.2142/biophysics.8.79
39. • 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
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    • D453-D460
    • 2012
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40. • GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.
    • Kinjo, A.R., Nakamura, H.
    • Biophysics
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    • 79-94
    • 2012
    • 10.2142/biophysics.8.79
41. • The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future.
    • Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.
    • Structure
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    • 391-396
    • 2012
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    • 10.1016/j.str.2012.01.010
42. • 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
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    • 2012
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43. • The future of the protein data bank.
    • Berman, H.M., Kleywegt, G.J., Nakamura, H., Markley, J.L.
    • Biopolymers
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    • 218-222
    • March
    • 2013
    • 10.1002/bip.22132
44. • 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
45. • SeSAW: balancing sequence and structural information in protein functional mapping.
    • Standley, D.M., Yamashita, R., Kinjo, A.R., Toh, H., Nakamura, H.
    • Bioinformatics
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    • 1258-1259
    • 2010
    • 20299324
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46. • 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
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    • 2010
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    • 10.1016/j.jmb.2010.04.028
47. • A comparative study of conservation and variation scores.
    • Johansson, F., Toh, H.
    • BMC Bioinformatics
    • 11
    • 388
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    • 10.1186/1471-2105-11-388
48. • Relative von neumann entropy for evaluating amino Acid conservation.
    • Johansson, F., Toh, H.
    • J Bioinform Comput Biol
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    • 5
    • 809-823
    • 2010
    • 10.1142/S021972001000494X
49. • PDBj Mine: Design and implementation of relational database interface for Protein Data Bank Japan.
    • Kinjo, A.R., Yamashita, R., Nakamura, H.
    • Database
    • 2010
    • baq021
    • 2010
    • 10.1093/database/baq021
50. • Comprehensive structural classification of ligand-binding motifs in proteins.
    • Kinjo, A.R., Nakamura, H.
    • Structure
    • 17
    • 2
    • 234-246
    • 2009
    • 19217394
    • 10.1016/j.str.2008.11.009
51. • Outcome of a Workshop on Applications of Protein Models in Biomedical Research.
    • Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D., Brenner, S.E., Burley, S.K., Das, R., Dokholyan, N.V., Dunbrack Jr., R.L., Fidelis, K., Fiser, A., Godzik, A., Huang, Y.J., Humblet, C., Jacobson, M.P., Joachimiak, A., Krystek Jr., S.R., Kortemme, T., Kryshtafovych, A., Montelione, G.T., Moult, J., Murray, D., Sanchez, R., Sosnick, T.R., Standley, D.M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J.D., Wilson, I.A.
    • Structure
    • 17
    • 2
    • 151-159
    • 2009
    • 19217386
    • 10.1016/j.str.2008.12.014
52. • Data Deposition and Annotation at the Worldwide Protein Data Bank.
    • Dutta, S., Burkhardt, K., Young, J., Swaminathan, G.J., Matsuura, T., Henrick, K., Nakamura, H., Berman, H.M.
    • Mol. Biotechnol.
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    • 1-13
    • 2009
    • 19082769
    • 10.1007/s12033-008-9127-7
53. • Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model.
    • Kawabata, T.
    • Biophys J
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    • 4643-4658
    • 2008
    • 18708469
    • 10.1529/biophysj.108.137125
54. • Recent developments in the MAFFT multiple sequence alignment program.
    • Katoh, K., Toh, H.
    • Brief. Bioinform.
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    • 286-298
    • 2008
    • 18372315
    • 10.1093/bib/bbn013
55. • Structure-based functional annotation of protein sequences guided by comparative models.
    • Standley, D.M., Kinjo, A.R., Lis, M., van der Giezen, M., Nakamura, H.
    • Proceedings of the Second International Symposium on Optimization and Systems Biology (ed. Luonan Chen) Lijiang China.
    • 395-403
    • 2008
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56. • BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.
    • Markley, J.L., Ulrich, E.L., Berman, H.M., Henrick, K., Nakamura, H., Akutsu, H.
    • J. Biomol. NMR
    • 40
    • 3
    • 153-155
    • 2008
    • 18288446
    • 10.1007/s10858-008-9221-y
57. • Remediation of the protein data bank archive.
    • Henrick, K., Feng, Z., Bluhm, W.F., Dimitropoulos, D., Doreleijers, J.F., Dutta, S., Flippen-Anderson, J.L., Ionides, J., Kamada, C., Krissinel, E., Lawson, C.L., Markley, J.L., Nakamura, H., Newman, R., Shimizu, Y., Swaminathan, J., Velankar, S., Ory, J., E. Ulrich, E.L., Vranken, W., Westbrook, J.D., Yamashita, R., Yang, H., Young, J., Yousufuddin, M., Berman, H.M.
    • Nucleic Acids Res.
    • 36
    • Database issue
    • D426-D433
    • 2008
    • 18073189
    • 10.1093/nar/gkm937
58. • BioMagResBank.
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