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PDBjの引用文献

PDBj自体を引用される場合は、文献リストの (29) (30) (36) をご利用ください。

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サービス名URL引用文献
PDB検索（PDBj Mine）pdbj.org/mine (29) (30) (36)
化合物検索（Chemie）pdbj.org/chemie-search (29) (30)
Mine 2 RDB pdbj.org/rdb/search
Local install
 (29) (30) (36)
BMRB検索bmrbj.pdbj.org (30)
Sequence Navigatorpdbj.org/seqnavi (36)
DASH（Structure Navigator後継）sysimm.org/dash/ (10)
EM Navigatorpdbj.org/emnavi (29) (30)
Omokage検索pdbj.org/emnavi/omo-search.php (26)
wwPDB/RDFrdf.wwpdb.org (19)
SeSAWsysimm.org/sesaw.2.0/ (15)
Ligand Binding Sites (GIRAF)pdbj.org/giraf (8) (13) (14) (18)
jV : 3次元分子ビューアpdbj.org/jv (3)
Molmil: WebGL分子ビューア pdbj.org/molmil2
source code
Molmil app
 (25) (36)
万見（Yorodumi）pdbj.org/emnavi/quick.php (29) (30)
ASHsysimm.org/ash_service/ (5) (10) (11)
MAFFTashsysimm.org/MAFFTash/ (11)
NMRToolBoxbmrbj.pdbj.org/en/nmr_tool_box.html (7) (17) (23)
gmfitpdbj.org/gmfit (12)
CRNPREDpdbj.org/crnpred (4) (6)
Spannersysimm.org/spanner/ (16)
SFASsysimm.org/pipeline7/-
HOMCOShomcos.pdbj.org (24) (36)
eF-site pdbj.org/eF-site/ (1) (3)
eF-seek
eF-surf		 pdbj.org/eF-seek/top.do
pdbj.org/eF-surf/top.do 		(22)
ProMode Elasticpdbj.org/promode-elastic (2) (21) (28)
hGTOPpford.info/hGTOP_db-
eProtSpdbj.org/eprots-
PDBj入門
今月の分子・ゲーム・ペーパーモデル		 numon.pdbj.org/mom
numon.pdbj.org/games
numon.pdbj.org/papermodel
 (36)
OneDep（PDB、EMDB、BMRBへの登録）deposit-pdbj.wwpdb.org/deposition (27)
フォーマット変換mmcif.pdbj.org/converter/index.php-
PDBx/mmCIFエディタpdbj.org/cif-editor/ (32) (36)
Biological Structure Model Archivebsma.pdbj.org (33)
RDFポータルrdfportal.org doi:10.1093/database/bay123

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。


文献一覧

  1. 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 May 27 2024 baae041 PMID: 38803272 doi: 10.1093/database/baae041
  2. 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. J Mol Biol. 168546 2024 PMID: 38508301 doi: 10.1016/j.jmb.2024.168546
  3. Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank. Baskaran K, Ploskon E, Tejero R, Yokochi M, Harrus D, Liang Y, Peisach E, Persikova I, Ramelot TA, Sekharan M, Tolchard J, Westbrook JD, Bardiaux B, Schwieters CD, Patwardhan A, Velankar S, Burley SK, Kurisu G, Hoch JC, Montelione GT, Vuister GW, Young JY Structure S0969-2126(24)00050-9 March 14 2024 PMID: 38490206 doi: 10.1016/j.str.2024.02.011
  4. 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 11 2 140-151 March 1 2024 PMID: 38358351 doi: 10.1107/S2052252524001246
  5. EMDB-the Electron Microscopy Data Bank. wwPDB Consortium Nucleic Acids Res. 52 D1 D456–D465 Jan 5 2024 PMID: 37994703 doi: 10.1093/nar/gkad1019
  6. 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 79 9 792-795 Sep 1 2023 PMID: 37561405 doi: 10.1107/S2059798323006381
  7. 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. 435 14 168021 Jul 15 2023 PMID: 36828268 doi: 10.1016/j.jmb.2023.168021
  8. 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 Nucleic Acids Res. 51 D1 D368-D376 Jan 6 2023 PMID: 36478084 doi: 10.1093/nar/gkac1050
  9. 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 6 1233-1238 Dec 9 2022 PMID: 36532871 doi: 10.1007/s12551-022-01021-w
  10. 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. 434 11 167599 Jun 15 2022 PMID: 35460671 doi: 10.1016/j.jmb.2022.167599
  11. 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 31: 173–186. (2022) PMID: 34664328 doi: 10.1002/pro.4211
  12. 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 PMID: 33978738 doi: 10.1093/glycob/cwab039
  13. The Protein Data Bank Archive. Sameer Velankar, Stephen K Burley, Genji Kurisu, Jeffrey C Hoch, John L Markley Methods in molecular biology 2305 3-21 2021 PMID: 33950382 doi: 10.1007/978-1-0716-1406-8_1
  14. 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) PMID: 32026396 doi: 10.1007/s12551-020-00632-5
  15. Protein Data Bankで利用するPDBx/mmCIF形式について
    Gert-Jan BEKKER, 工藤 高裕, 池川 恭代, 山下 鈴子, 栗栖 源嗣
    日本結晶学会誌 61(3): 159-160 (2019) doi:10.5940/jcrsj.61.159
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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)
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. 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]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
  44. 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]
  45. 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]
  46. 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]

PDBエントリーの引用について

各PDBエントリーを引用される場合は、以下の様式をご利用ください。

  • 対応するPrimary citation（引用文献）があるPDB構造は、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構造は、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

作成日: 2020-10-30 (最終更新日: 1 month ago)2024-06-06

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