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Publications

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2014

  • Systematic Detection of Internal Symmetry in Proteins Using CE-Symm
    (2014) Journal of Molecular Biology 426: 2255-2268 doi:10.1016/j.jmb.2014.03.010
  • Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank
    (2014) Biopolymers 101:659-668 doi:10.1002/bip.22434
  • Establishing the Next Generation of the Protein Data Bank
    (2014) The Winnower doi:10.15200/winn.140076.68556


2013

  • The RCSB Protein Data Bank: new resources for research and education
    (2013) Nucleic Acids Research 41: D475-D482 doi:10.1093/nar/gks1200
  • Recommendations of the wwPDB NMR Validation Task Force
    (2013) Structure 21: 1563-1570 doi:10.1016/j.str.2013.07.021
  • How community has shaped the Protein Data Bank
    (2013) Structure 21: 1485-1491 doi:10.1016/j.str.2013.07.010
  • Revealing structural views of biology
    (2013) Biopolymers 99: 817-824 doi:10.1002/bip.22338
  • Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB Structure
    (2013) Structure 21: 875-881 doi:10.1016/j.str.2013.04.020
  • Trendspotting in the Protein Data Bank
    (2013) FEBS Lett. 587: 1036-45 doi:10.1016/j.febslet.2012.12.029
  • The Future of the Protein Data Bank
    (2013) Biopolymers 99: 218-222 doi:10.1002/bip.22132
  • 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
  • Comment on On the propagation of errors by Jaskolski
    (2013) Acta Cryst D69: 2297 doi:10.1107/S090744491302917X
  • Chemical annotation of small and peptide-like molecules at the Protein Data Bank
    (2013) Database doi:10.1093/database/bat079
  • The Twists and Turns of DNA
    (2013) The Biologist 60: 18-22.


2012

  • Illustrating the Machinery of Life: Viruses
    (2012) Biochemistry and Molecular Biology Education 40: 291-296 doi:10.1002/bmb.20636
  • Putting proteins in context: scientific illustrations bring together information from diverse sources to provide an integrative view of the molecular biology of cells
    (2012) Bioessays 34(9):718-20 doi:10.1002/bies.201200072
  • Creating a community resource for protein science
    (2012) Protein Science 21: 1587-1596 doi:10.1002/pro.2154
  • BioJava: an open-source framework for bioinformatics in 2012
    (2012) Bioinformatics 28: 2693-2695 doi:10.1093/bioinformatics/bts494
  • Outcome of the first electron microscopy validation task force meeting
    (2012) Structure 20: 205-214 doi:10.1016/j.str.2011.12.014
  • The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future
    (2012) Structure 20: 391-396 doi:10.1016/j.str.2012.01.010
  • The Worldwide Protein Data Bank
    (2012) In International Tables for X-Ray Crystallography, Volume F: Crystallography of biological macromolecules
    E. Arnold, D. M. Himmel & M. G. Rossmann, editors Springer, Dordrecht, The Netherlands, pp. 827-832 doi:10.1107/97809553602060000111
  • Circular Permutation in Proteins
    (2012) PLoS Comput Bio 8: e1002445 doi:10.1371/journal.pcbi.1002445
  • The Protein Data Bank
    (2012) in Leadership in Science and Technology: A Reference Handbook, William Sims Bainbridge, editor SAGE Publications, Inc., Thousand Oaks, CA., volume 2, pages 661-675.


2011

  • The RCSB Protein Data Bank: redesigned web site and web services
    (2011) Nucleic Acids Res. 39: D392-D401 doi:10.1093/nar/gkq1021
  • Atomic evidence: the foundations of structural molecular biology
    (2011) Science Progress 94: 414-430 doi:10.3184/003685011X13201799666745
  • The evolution of the Protein Data Bank (part of special essay collection on the 40th anniversary of the PDB)
    (2011) Nature Structural & Molecular Biology 18: 1310 doi:10.1038/nsmb1211-1304
  • Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction
    (2011) Proteins: Structure, Function, and Bioinformatics 79: 6-20 doi:10.1002/prot.23196
  • A new generation of crystallographic validation tools for the Protein Data Bank
    (2011) Structure 19: 1395-1412 doi:10.1016/j.str.2011.08.006
  • Miniseries: Illustrating the machinery of life: Eukaryotic cell panorama
    (2011) Biochem Mol Biol Educ. 39:91-101 doi:10.1002/bmb.20494
  • The evolution of the RCSB Protein Data Bank website
    (2011) WIREs Computational Molecular Science 1: 782-789 doi:10.1002/wcms.57
  • The RCSB Protein Data Bank: site functionality and bioinformatics use cases
    (2011) NCI-Nature Pathway Interaction Database doi:10.1038/pid.2011.1
  • Quality assurance for the query and distribution systems of the RCSB Protein Data Bank
    (2011) Database doi:10.1093/database/bar003


2010

  • The Protein Data Bank: Exploring Biomolecular Structure
    (2010) Nature Education 3:39.
  • Precalculated Protein Structure Alignments at the RCSB PDB website
    (2010) Bioinformatics 26: 2983-2985 doi: 10.1093/bioinformatics/btq572
  • Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences
    (2010) J. Appl. Cryst. 43:1224-1229 doi:10.1107/S002188981002371X
  • Getting the Most Out of the Protein Data Bank
    (2010) The Journal of Biocommunication 35: E52-E57.
  • dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment
    (2010) BMC Bioinformatics 11:310. doi:10.1186/1471-2105-11-310
  • Integration of open access literature into the RCSB Protein Data Bank Using BioLit
    (2010) BMC Bioinformatics 11:220. doi:10.1186/1471-2105-11-220
  • Will Widgets and Semantic Tagging Change Computational Biology?
    (2010) PLoS Comput Biol 6(2): e1000673. doi:10.1371/journal.pcbi.1000673


2009

  • Data Deposition and Annotation at the Worldwide Protein Data Bank
    (2009) Mol Biotechnol 42:1-13. doi: 10.1007/s12033-008-9127-7
  • The PDB format, mmCIF formats, and other data formats in Structural Bioinformatics, second edition
    (2009) Gu and Bourne, eds. John Wiley & Sons, Inc., Hoboken, NJ, pp 271-291
  • The Worldwide Protein Data Bank in Structural Bioinformatics, second edition
    (2009) Gu and Bourne, eds. John Wiley & Sons, Inc., Hoboken, NJ, pp 293-303.
  • Outcome of a Workshop on Applications of Protein Models in Biomedical Research
    (2009) Structure 17: 151-159. doi: 10.1016/j.str.2008.12.014


2008

  • Representation of viruses in the remediated PDB archive
    (2008) Acta Cryst. D64: 874-882 doi: 10.1107/S0907444908017393
  • Interesting Structures: Education and Outreach at the RCSB Protein Data Bank
    (2008) PLoS Biology 6:e117. doi: 10.1371/journal.pbio.0060117
  • Data deposition and annotation at the Worldwide Protein Data Bank
    (2008) Methods in Molecular Biology, vol. 426 doi: 10.1007/s12033-008-9127-7
  • BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions
    (2008) J Biomol NMR 40(3): 153-155 doi: 10.1007/s10858-008-9221-y
  • Remediation of the Protein Data Bank archive
    (2008) Nucleic Acids Research 36: D426-433. doi: 10.1093/nar/gkm937
  • The Protein Data Bank: a historical perspective
    (2008) Acta Cryst. A64: 88-95. doi: 10.1107/S0108767307035623


2007

  • Using the Tools and Resources of the RCSB Protein Data Bank
    (2007) Current Protocols in Bioinformatics 1.9.1-1.9.24. doi: 10.1002/0471250953.bi0109s20
  • A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing
    (2007) Proteins 69(3): 449-65. doi: 10.1002/prot.21507
  • Realism about PDB
    (2007) Nature Biotechnology 25: 845-846. doi: 10.1038/nbt0807-845
  • The Research Collaboratory for Structural Bioinformatics Protein Data Bank
    (2007) Comprehensive Medicinal Chemistry II, Vol. 3, Drug Discovery Technologies, H. Kubinyi, Ed, Elsevier, Oxford, UK pp. 373-388.
  • The Worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    (2007) Nucleic Acids Res. 35(Database issue): D301-3. doi: 10.1093/nar/gkl971


2006

  • A Biocurator Perspective: Annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank
    (2006) PLoS Comput Biol 2(10): e99 doi: 10.1371/journal.pcbi.0020099
  • Archiving structural models of biological macromolecules: outcome of a workshop on biological macromolecular structure models
    (2006) Structure, 14: 1211-1217 doi: 10.1016/j.str.2006.06.005
  • Partitioning protein structures into domains: Why is it so difficult?
    (2006) J Mol Biol, 361(3): 562-90. doi: 10.1016/j.jmb.2006.05.060
  • Reflections on the science and law of structural biology, genomics, and drug development
    (2006) UCLA Law Review, 53: 871 - 908
  • The RCSB PDB information portal for structural genomics
    (2006) Nucleic Acids Research, Vol. 34, Database issue D302-D305 doi: 10.1093/nar/gkj120


2005

  • Using the Tools and Resources of the RCSB Protein Data Bank
    (2005) Current Protocols in Bioinformatics 1.9.1-1.9.40. doi: 10.1002/0471250953.bi0109s20
  • The Molecular Biology Toolkit (MBT): A Modular Platform for Developing Molecular Visualization Applications
    (2005) BMC Bioinformatics, 6: 21. doi:10.1186/1471-2105-6-21
  • Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.
    (2005) PLoS Comp Biol 1(3): e31. doi:10.1371/journal.pcbi.0010031
  • PDBML: the representation of archival macromolecular structure data in XML
    (2005) Bioinformatics 21, pp. 988-992. doi: 10.1093/bioinformatics/bti082
  • Large Macromolecular Complexes in the Protein Data Bank: A Status Report
    (2005) Structure 13, pp. 381-388. doi:10.1016/j.str.2005.01.008
  • The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema
    (2005) Nucl. Acids Res 33: D233-D237. doi:10.1093/nar/gki057
  • DDL2 dictionary, in International Tables for Crystallography
    (2005) J.D. Westbrook and S.R. Hall, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 473-481. doi:10.1107/97809553602060000750
  • The Macromolecular dictionary (mmCIF), in International Tables for Crystallography, Volume G
    (2005) P.M.D. Fitzgerald, J.D. Westbrook, P.E. Bourne, B. McMahon, K.D. Watenpaugh, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 295-443. doi:10.1107/97809553602060000107
  • Classification and use of macromolecular data, in International Tables for Crystallography, Volume G
    (2005) P.M.D. Fitzgerald, J.D. Westbrook, P.E. Bourne, B. McMahon, K.D. Watenpaugh, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors., Springer: Dordrecht, The Netherlands. p. 144-198. doi:10.1107/97809553602060000107
  • Specification of a relational Dictionary Definition Language (DDL2), in International Tables for Crystallography, Volume G
    (2005) J.D. Westbrook, H.M. Berman, and S.R. Hall, , G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 61-72. doi:10.1107/97809553602060000107
  • The use of mmCIF architecture for PDB data management, in International Tables for Crystallography, Volume G
    (2005) J. Westbrook, H. Yang, Z. Feng, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors., Springer: Dordrecht, The Netherlands. p. 539-543. doi:10.1107/97809553602060000107
  • The Protein Data Bank exchange data dictionary, in International Tables for Crystallography, Volume G
    (2005) J. Westbrook, K. Henrick, E.L. Ulrich, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 195-198. doi:10.1107/97809553602060000107
  • Image dictionary (imgCIF), in International Tables for Crystallography, Volume G
    (2005) A.P. Hammersley, H.J. Bernstein, and J.D. Westbrook, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 444-459. doi:10.1107/97809553602060000107
  • Specification of the Crystallographic Information File, in International Tables for Crystallography, Volume G
    (2005) S.R. Hall and J.D. Westbrook, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 20-36. doi:10.1107/97809553602060000107
  • Formal specification of the Crystallographic Information File, in International Tables for Crystallography, Volume G
    (2005) S.R. Hall, N. Spadaccini, I.D. Brown, H.J. Bernstein, J.D. Westbrook, and B. McMahon, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 25-36. doi:10.1107/97809553602060000107


2004

  • TargetDB: a target registration database for structural genomics projects
    (2004) Bioinformatics 20, pp. 2860-2862. doi: 10.1093/bioinformatics/bth300
  • Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
    (2004) Acta Cryst. D60, pp. 1833-1839. doi: 10.1107/S0907444904019419
  • Ligand Depot: a data warehouse for ligands bound to macromolecules
    (2004) Bioinformatics 20, pp. 2153-2155. doi: 10.1093/bioinformatics/bth214
  • The Impact of Structural Genomics on the Protein Data Bank
    (2004) Am. J. PharmacoGenomics 4, pp. 247-252.
  • The Protein Data Bank and lessons in data management
    (2004) Briefings in Bioinformatics 5, pp 23-30. doi: 10.1093/bib/5.1.23
  • The PDB: A case study in management of community data
    (2004) Published in the inaugural issue of Current Proteomics. Current Proteomics 1, pp. 49-57. doi: 10.2174/1570164043488252


2003

  • Validation of protein structures for the PDB
    (2003) Methods Enzymol. 374, pp. 370-85. doi: 10.1016/S0076-6879(03)74017-8
  • The distribution and query systems of the RCSB Protein Data Bank
    (2003) Nucleic Acids Research, 32, pp. D223-5. doi: 10.1093/nar/gkh096
  • Announcing the worldwide Protein Data Bank
    (2003) Nature Structural Biology, 10 (12), p. 980. doi: 10.1038/nsb1203-980
  • The Protein Data Bank and structural genomics
    (2003) Nucleic Acids Research 31, pp. 489-491. doi: 10.1093/nar/gkg068
  • The Protein Data Bank
    (2003) P. E. Bourne and H. Weissig. Hoboken, NJ, John Wiley & Sons, Inc. pp. 181-198.
  • The PDB format, mmCIF formats and other data formats.
    (2003) P. E. Bourne and H. Weissig. Hoboken, NJ, John Wiley & Sons, Inc. pp. 161-179. 10.1038/80734


2002

  • An ontology driven architecture for derived representations of macromolecular structure
    (2002) Bioinformatics 18 (9), pp. 1280-1281. Oxford University Press. doi: 10.1093/bioinformatics/18.9.1280
  • The CCPN project: an interim report on a data model for the NMR community
    (2002) Nature Structural Biology 9 (6), pp. 416-418. doi: 10.1038/nsb0602-416
  • Protein Structures: From Famine to Feast
    (2002) American Scientist 90 (4), pp. 350 - 359. doi: 10.1511/2002.4.350
  • The Protein Data Bank
    (2002) Acta Cryst. D 58 (6:1), pp. 899-907. doi: 10.1107/S0907444902003451
  • Protein structure resources
    (2002) Acta Cryst. D 58 (6:1), pp. 908-915. doi: 10.1107/S0907444902003906
  • The Protein Data Bank: unifying the archive
    (2002) Nucleic Acids Research, 30 (1), pp. 245-248. doi: 10.1093/nar/30.1.245


2001

  • The Protein Data Bank, 2001 -
    (2001) In International Tables for Crystallography (M. G. Rossman & E. Arnold, eds.), Vol. F. Crystallography of Biological Macromolecules, pp. 675-662. Kluwer Academic Publishers, Dordrecht.
  • The PDB data uniformity project
    (2001) Nucleic Acids Research, 29: 214-218. doi: 10.1093/nar/29.1.214


2000

  • The Protein Data Bank
    (2000) Nucleic Acids Research 28: 235-242. doi: 10.1093/nar/28.1.235
  • The Protein Data Bank and the challenge of structural genomics
    (2000) Nature Structural Biology, 7 (11), pp. 957-959. doi: 10.1038/80734