wwPDB Publications

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. Daughter, 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