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wwPDB Publications

2024

  • Preeti Choudhary, Zukang Feng, John Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Y. Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley; PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank. Database (2024): baae041 doi: 10.1093/database/baae041
  • 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. Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank. Structure (2024) PMID: 38490206. doi: 10.1016/j.str.2024.02.011
  • Sebastian Bittrich, Adam Midlik, Mihaly Varadi, Sameer Velankar, Stephen K. Burley, Jasmine Y. Young, David Sehnal, Brinda Vallat. Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit. CURRENT PROTOCOLS (2024). doi: 10.1002/cpz1.1099

2023

  • The wwPDB Consortium (2023) EMDB- the Electron Microscopy Data Bank Nucleic Acids Research gkad1019 doi: 10.1093/nar/gkad1019
  • Preeti Choudhary, Zukang Feng, John Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Y. Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley; PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank (2023) bioRxiv doi: 10.1101/2023.10.24.563739
  • Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Cathy Lawson, Alexis Rohou, Peter B. Rosenthal, Sriram Subramaniam, Maya Topf, Sanja Abbott, Philip R. Baldwin, John M. Berrisford, Gérard Bricogne, Preeti Choudhary, Tristan I. Croll, Radostin Danev, Sai J. Ganesan, Timothy Grant, Aleksandras Gutmanas, Richard Henderson, J. Bernard Heymann, Juha T. Huiskonen, Andrei Istrate, Takayuki Kato, Gabriel C. Lander, Shee-Mei Lok, Steven J. Ludtke, Garib N. Murshudov, Ryan Pye, Grigore D. Pintilie, Jane S. Richardson, Carsten Sachse, Osman Salih, Sjors H.W. Scheres, Gunnar F. Schroeder, Carlos Oscar S. Sorzano, Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar (2024) Community recommendations on cryoEM data archiving and validation. IUCrJ doi: 10.1107/S2052252524001246
  • Wenqing Xu, Sameer Velankar, Ardan Patwardhan, Jeffrey C. Hoch, Stephen K. Burley, Genji Kurisu. (2023) Announcing launch of Protein Data Bank China (PDBc) as an Associate Member of the Worldwide Protein Data Bank (wwPDB) Partnership Acta Cryst. D doi: 10.1107/S2059798323006381

2022

  • John D. Westbrook, Jasmine Y. Young, Chenghua Shao, Zukang Feng, Vladimir Guranovic, Catherine L. Lawson, Brinda Vallat, Paul D. Adams, John M Berrisford, Gerard Bricogne, Kay Diederichs, Robbie P. Joosten, Peter Keller, Nigel W. Moriarty, Oleg V. Sobolev, Sameer Velankar, Clemens Vonrhein, David G. Waterman, Genji Kurisu, Helen M. Berman, Stephen K. Burley, Ezra Peisach. (2022) PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology. JMB doi: 10.1016/j.jmb.2022.167599

2021

  • Chenghua Shao, Zukang Feng, John D Westbrook, Ezra Peisach,John Berrisford, Yasuyo Ikegawa, Genji Kurisu, Sameer Velankar,Stephen K Burley and Jasmine Y Young. (2021) Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. Glycobiology 1–15: doi: 10.1093/glycob/cwab039
  • Jasmine Y. Young, John Berrisford & Minyu Chen. (2021) wwPDB biocuration: on the front line of structural biology. Nature Methods 18: 431–432 doi: 10.1038/s41592-021-01137-z
  • 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 and Jasmine Y. Young. (2021) Enhanced Validation of Small-Molecule Ligands and Carbohydrates in the Protein Data Bank. Structure doi: 10.1016/j.str.2021.02.004

2019

  • Paul D. Adams, Pavel V. Afonine, Kumaran Baskaran, Helen M. Berman, John Berrisford, Gerard Bricogne, David G. Brown, Stephen K. Burley, Minyu Chen, Zukang Feng, Claus Flensburg, Aleksandras Gutmanas, Jeffrey C. Hoch, Yasuyo Ikegawa, Yumiko Kengaku, Eugene Krissinel,l Genji Kurisu, Yuhe Liang, Dorothee Liebschner, Lora Mak, John L. Markley, Nigel W. Moriarty, Garib N. Murshudov, Martin Noble, Ezra Peisach, Irina Persikova, Billy K. Poon, Oleg V. Sobolev, Eldon L. Ulrich, Sameer Velankar, Clemens Vonrhein, John Westbrook, Marcin Wojdyr, Masashi Yokochij and Jasmine Y. Young. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB) (2019) Volume 75, Pages 451-454 doi: 10.1107/S2059798319004522

2018

  • wwPDB consortium (2018) Protein Data Bank: the single global archive for 3D macromolecular structure data Nucleic Acids Research: gky949 doi: 10.1093/nar/gky949
  • J.Y. Young, J. D. Westbrook, Z. Feng, E. Peisach, I. Persikova, R. Sala, S. Sen, J. M. Berrisford, G. J. Swaminathan, T. J. Oldfield, A. Gutmanas, R. Igarashi, D. R. Armstrong, K. Baskaran, L. Chen, M. Chen, A. R. Clark, L. D. Costanzo, D. Dimitropoulos, G. Gao, S. Ghosh, S. Gore, V. Guranovic, P. M. S. Hendrickx, B. P. Hudson, Y. Ikegawa, Y. Kengaku, C. L. Lawson, Y. Liang, L. Mak, A. Mukhopadhyay, B. Narayanan, K. Nishiyama, A. Patwardhan, G. Sahni, E. Sanz-García, J. Sato, M. R. Sekharan, C. Shao, O. S. Smart, L. Tan, G. v. Ginkel, H. Yang, M. A. Zhuravleva, J. L. Markley, H. Nakamura, G. Kurisu, G. J. Kleywegt, S. Velankar, H. M. Berman, S. K. Burley (2018) Worldwide Protein Data Bank biocuration supporting open sccess to high-quality 3D structural biology data Database 2018: bay002 doi: 10.1093/database/bay002

2017

  • S. Gore, E. Sanz Garcia, P. M. S. Hendrickx, A. Gutmanas, J. D. Westbrook, H. Yang, Z. Feng, K. Baskaran, J. M. Berrisford, B. P. Hudson, Y. Ikegawa, N. Kobayashi, C. L. Lawson, S. Mading, L. Mak, A. Mukhopadhyay, T. J. Oldfield, A. Patwardhan, E. Peisach, G. Sahni, M. R. Sekharan, S. Sen, C. Shao, O. S. Smart, E. L. Ulrich, R. Yamashita, M. Quesada, J. Y. Young, H. Nakamura, J. L. Markley, H. M. Berman, S. K. Burley, S. Velankar, G. J. Kleywegt. (2017) Validation of the Structures in the Protein Data Bank. Structure 25: 1916-1927 doi: 10.1016/j.str.2017.10.009
  • S. K. Burley, G. Kurisu, J. L. Markley, H. Nakamura, S. Velankar, H. M. Berman, A. Sali, T. Schwede, J. Trewhella. (2017) PDB-Dev: A prototype system for depositing integrative/hybrid structural models. Structure 25: 1317-1318 doi: 10.1016/j.str.2017.08.001
  • S. K. Burley, H. M. Berman, G. J. Kleywegt, J. L. Markley, H. Nakamura, S. Velankar. (2017) Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive In Methods in Molecular Biology: Protein Crystallography Methods and Protocols (eds. A. Wlodawer, Z. Dauter, M. Jaskolski) Springer New York doi: 10.1007/978-1-4939-7000-1
  • J. Young, J. D. Westbrook, Z. Feng, R. Sala, E. Peisach, T. J. Oldfield, S. Sen, A. Gutmanas, D. R. Armstrong, J. M. Berrisford, L. Chen, M. Chen, L. Di Costanzo, D. Dimitropoulos, G. Gao, S. Ghosh, S. Gore, V. Guranovic, P. M. S. Hendrickx, B. P. Hudson, R. Igarashi, Y. Ikegawa, N. Kobayashi, C. L. Lawson, Y. Liang, S. Mading, L. Mak, M. S. Mir, A. Mukhopadhyay, A. Patwardhan, I. Persikova, L. Rinaldi, E. Sanz-Garcia, M. R. Sekharan, C. Shao, G. J. Swaminathan, L. Tan, E. L. Ulrich, G. Van Ginkel, R. Yamashita, H. Yang, M. A. Zhuravleva, M. Quesada, G. J. Kleywegt, H. M. Berman, J. L. Markley, H. Nakamura, S. Velankar, S. K. Burley. (2017) OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the Protein Data Bank (PDB) Archive. Structure 25: 536-545 doi: 10.1016/j.str.2017.01.004
  • The Global Life Sciences Data Resources (GLSDR) Working Group: W. Anderson, R. Apweiler, A. Bateman, G.A. Bauer, H. Berman, J.A. Blake, N. Blomberg, S.K. Burley, G. Cochrane, V. Di Francesco, T. Donohue, C. Durinx, A. Game, E.D. Green, T. Gojobori, P. Goodhand, A. Hamosh, H. Hermjakob, M. Kanehisa, R. Kiley, J. McEntyre, R. McKibbin, S. Miyano, B. Pauly, N. Perrimon, M.A. Ragan, G. Richards, Y-Y. Teo, M. Westerfield, E. Westhof, P.F. Lasko (2017) Data management: A global coalition to sustain core data Nature 543: 179 doi: 10.1038/543179a
  • W. Anderson, R. Apweiler, A. Bateman, G.A. Bauer, H. Berman, J.A. Blake, N. Blomberg, S.K. Burley, G. Cochrane, V. Di Francesco, T. Donohue, C. Durinx, A. Game, E.D. Green, T. Gojobori, P. Goodhand, A. Hamosh, H. Hermjakob, M. Kanehisa, R. Kiley, J. McEntyre, R. McKibbin, S. Miyano, B. Pauly, N. Perrimon, M.A. Ragan, G. Richards, Y-Y. Teo, M. Westerfield, E. Westhof, P.F. Lasko (2017) Towards coordinated international support of core data resources for the life sciences bioRxiv doi: 10.1101/110825

2016

  • H. M. Berman, S. K. Burley, G. J. Kleywegt, J. L. Markley, H. Nakamura, S. Velankar. (2016) The archiving and dissemination of biological structure data. Curr Opin Struct Biol 40: 17-22 doi: 10.1016/j.sbi.2016.06.018
  • P. D. Adams, K. Aertgeerts, C. Bauer, J. A. Bell, H. M. Berman, T. N. Bhat, J. M. Blaney, E. Bolton, G. Bricogne, D. Brown, S. K. Burley, D. A. Case, K. L. Clark, T. Darden, P. Emsley, V. A. Feher, Z. Feng, C. R. Groom, S. F. Harris, J. Hendle, T. Holder, A. Joachimiak, G. J. Kleywegt, T. Krojer, J. Marcotrigiano, A. E. Mark, J. L. Markley, M. Miller, W. Minor, G. T. Montelione, G. Murshudov, A. Nakagawa, H. Nakamura, A. Nicholls, M. Nicklaus, R. T. Nolte, A. K. Padyana, C. E. Peishoff, S. Pieniazek, R. J. Read, C. Shao, S. Sheriff, O. Smart, S. Soisson, J. Spurlino, T. Stouch, R. Svobodova, W. Tempel, T. C. Terwilliger, D. Tronrud, S. Velankar, S. C. Ward, G. L. Warren, J. D. Westbrook, P. Williams, H. Yang, J. Young. (2016) Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure 24: 502-508 doi: 10.1016/j.str.2016.02.017

2015

  • A. Sali, T. Schwede, J. Trewhella, H. M. Berman, G. Kleywegt, S. K. Burley, J. Markley, H. Nakamura, P. D. Adams, A. Bonvin, W. Chiu, M. Dal Peraro, F. Di Maio, T. E. Ferrin, K. Grunewald, A. Gutmanas, R. Henderson, G. Hummer, K. Iwasaki, G. Johnson, C. L. Lawson, J. Meiler, M. A. Marti-Renom, G. T. Montelione, M. Nilges, R. Nussinov, A. Patwardhan, J. Rappsilber, R. J. Read, H. Saibil, G. F. Schroder, C. Schwieters, C. A. M. Seidel, D. Svergun, M. Topf, E. Ulrich, S. Velankar, J. Westbrook (2015) Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop Structure 23: 1156—1167 doi: 10.1016/j.str.2015.05.013
  • A. Gutmanas, P.D. Adams, B. Bardiaux, H.M. Berman, D.A. Case, R.H. Fogh, P. Güntert, P.M.S. Hendrickx, T. Herrmann, G.J. Kleywegt, N. Kobayashi, O.F. Lange, J.L. Markley, G.T. Montelione, M. Nilges, T.J. Ragan, C.D. Schwieters, R. Tejero, E.L. Ulrich, S. Velankar, W.F. Vranken, J.R. Wedell, J. Westbrook, D.S. Wishart, G.W. Vuister (2015) NMR Exchange Format: a unified and open standard for representation of NMR restraint data Nature Structural & Molecular Biology 22: 433—434 doi: 10.1038/nsmb.3041

2014

  • J.D. Westbrook, C. Shao, Z. Feng, M. Zhuravleva, S. Velankar, J. Young (2014) The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank Bioinformatics doi: 10.1093/bioinformatics/btu789
  • S. Sen, J. Young, J. M. Berrisford, M. Chen, M. J. Conroy, S. Dutta, L. Di Costanzo, G. Gao, S. Ghosh, B. P. Hudson, R. Igarashi, Y. Kengaku, Y. Liang, E. Peisach, I. Persikova, A. Mukhopadhyay, B. C. Narayanan, G. Sahni, J. Sato, M. Sekharan, C. Shao, L. Tan, M. A. Zhuravleva (2014) Small molecule annotation for the Protein Data Bank doi: 10.1093/database/bau116
  • H. Berman, S. K. Burley, G. J. Kleywegt, H. Nakamura and J. L. Markley (2014) Response to "On prompt update of literature references in the Protein Data Bank" Acta Cryst D 70: 2780. doi: 10.1107/S1399004714020513
  • H. Berman, G. J. Kleywegt, H. Nakamura and J. L. Markley (2014) The Protein Data Bank archive as an open data resource Journal of Computer-Aided Molecular Design. doi: 10.1007/s10822-014-9770-y
  • S. Dutta, D. Dimitropoulos, Z. Feng, I. Persikova, S. Sen, C. Shao, J. Westbrook, J. Young, M.A. Zhuravleva, G.J. Kleywegt, H.M. Berman (2014) Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank Biopolymers 101:659-668 doi: 10.1002/bip.22434

2013

  • H. Berman, G. J. Kleywegt, H. Nakamura and J. L. Markley (2013) Comment on On the propagation of errors by Jaskolski (2013) Acta Cryst. D69: 2297. doi: 10.1107/S090744491302917X
  • H. Berman, G. J. Kleywegt, H. Nakamura and J. L. Markley. (2013) Comment on Timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013) Acta Cryst. D69: 2296. doi: 10.1107/S0907444913029168
  • H. M. Berman, G. J. Kleywegt, H. Nakamura, J. L. Markley. (2013) How community has shaped the Protein Data Bank Structure 21: 1485-1491 doi: 10.1016/j.str.2013.07.010
  • H. M. Berman, G. J. Kleywegt, H. Nakamura, J. L. Markley. (2013) The future of the protein data bank. Biopolymers 99: 218-222. doi: 10.1002/bip.22132

2012

  • H.M. Berman, K. Henrick, G. Kleywegt, H. Nakamura, J. Markley (2012) The Worldwide Protein Data Bank. In International Tables for X-Ray Crystallography (eds. E. Arnold, D.M. Himmel, M.G. Rossmann) Volume F: Crystallography of biological macromolecules, Springer, Dordrecht, The Netherlands, ch. 24.1, pp. 827-832 doi: 10.1107/97809553602060000896.
  • H. M. Berman, G. J. Kleywegt, H. Nakamura, J. L. Markley. (2012) The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future. Structure 20: 391-396. doi: 10.1016/j.str.2012.01.010

2010

  • H. M. Berman, G. J. Kleywegt, H. Nakamura, J. L. Markley, S. K. Burley. (2010) Safeguarding the integrity of protein archive. Nature 463: 425. doi: 10.1038/463425c

2009

  • S. Dutta, K. Burkhardt, J. Young, G. J. Swaminathan, T. Matsuura, K. Henrick, H. Nakamura, H. M. Berman. (2009) Data deposition and annotation at the worldwide Protein Data Bank. Mol Biotechnol 42: 1-13. doi: 10.1007/s12033-008-9127-7
  • H. M. Berman, K. Henrick, H. Nakamura, J. L. Markley. (2009). Chapter 11 The Worldwide Protein Data Bank. In Structural Bioinformatics, Second Edition (J. Gu & P. E. Bourne, eds.), pp. 293-303. John Wiley & Sons, Inc., Hoboken, NJ.

2008

  • J. L. Markley, E. L. Ulrich, H. M. Berman, K. Henrick, H. Nakamura, H. Akutsu. (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 40: 153-155. doi: 10.1007/s10858-008-9221-y
  • C. L. Lawson, S. Dutta, J. D. Westbrook, K. Henrick, H. M. Berman. (2008) Representation of viruses in the remediated PDB archive. Acta Cryst. D64: 874-882. doi: 10.1107/S0907444908017393
  • K. Henrick, Z. Feng, W. F. Bluhm, D. Dimitropoulos, J. F. Doreleijers, S. Dutta, J. L. Flippen-Anderson, J. Ionides, C. Kamada, E. Krissinel, C. L. Lawson, J. L. Markley, H. Nakamura, R. Newman, Y. Shimizu, J. Swaminathan, S. Velankar, J. Ory, E. L. Ulrich, W. Vranken, J. Westbrook, R. Yamashita, H. Yang, J. Young, M. Yousufuddin, H. M. Berman. (2008) Remediation of the Protein Data Bank Archive. Nucleic Acids Res 36: D426-D433. doi: 10.1093/nar/gkm937
  • S. Dutta, K. Burkhardt, G. J. Swaminathan, T. Kosada, K. Henrick, H. Nakamura, H. M. Berman. (2008). Data deposition and annotation at the Worldwide Protein Data Bank. In Methods in Molecular Biology (B. Kobe, M. Guss & T. Huber, eds.), Vol. 426: Structural Proteomics: High-Throughput Methods, pp. 81-101. Humana Press, Totowa, NJ.

2007

  • H. M. Berman, K. Henrick, H. Nakamura, J. L. Markley. (2007) The Worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35: D301-303. doi: 10.1093/nar/gkl971
  • H. Berman, K. Henrick, H. Nakamura, J. Markley, P. Bourne, J. Westbrook. (2007) Realism about PDB. Nature Biotechnology 25: 845-846. doi: 10.1038/nbt0807-845

2006

  • H. M. Berman, K. Henrick, H. Nakamura, E. Arnold. (2006) Is one solution good enough? (response). Nature Structural & Molecular Biology 13: 185.

2005

  • K. Henrick, H. M. Berman, H. Nakamura. (2005). The Protein Data Bank and the wwPDB. In Encyclopedia of Genomics, Proteomics, and Bioinformatics (L. B. Jorde, P. F. R. Little, M. J. Dunn & S. Subramaniam, eds.), Vol. 7, pp. 3335-3339. John Wiley & Sons Ltd, Chichester.

2003

  • H. M. Berman, K. Henrick, H. Nakamura. (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10: 980. doi: 10.1038/nsb1203-980