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wwPDB Publications

  • H. M. Berman, K. Henrick, H. Nakamura. (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10: 980.
  • 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.
  • H. M. Berman, K. Henrick, H. Nakamura, E. Arnold. (2006) Is one solution good enough? (response). Nature Structural & Molecular Biology 13: 185.
  • H. Berman, K. Henrick, H. Nakamura, J. Markley, P. Bourne, J. Westbrook. (2007) Realism about PDB. Nature Biotechnology 25: 845-846.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • H. M. Berman, G. J. Kleywegt, H. Nakamura, J. L. Markley, S. K. Burley. (2010) Safeguarding the integrity of protein archive. Nature 463: 425.
  • 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.
  • 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. (2013) The future of the protein data bank. Biopolymers 99: 218-222.
  • 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. 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.
  • 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.
  • 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


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