wwPDB Publications

2017

  • 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