Home LiteratureArticle Details
PMID: 26095030 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

Structure (London, England : 1993) ·Vol. 23 ·No. 7 ·2015-07-07 ·Pages 1156-67

Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD

Abstract

Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models?

MeSH Terms
Advisory Committees Computational Biology Databases, Protein Humans Models, Molecular Protein Conformation Proteins/chemistry
Chemicals
Proteins
Authors & Affiliations
38 authors, click to expand affiliations / ORCID
Sali Andrej
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall Room 503B, University of California, San Francisco, 1700 4(th) Street, San Francisco, CA 94158-2330, USA. Electronic address: sali@salilab.org.
Berman Helen M
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Schwede Torsten
Swiss Institute of Bioinformatics Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
Trewhella Jill
School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia.
Kleywegt Gerard
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Burley Stephen K
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
Markley John
BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.
Nakamura Haruki
Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Adams Paul
Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, UC Berkeley, Berkeley, CA 94720, USA.
Bonvin Alexandre M J J
Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
Chiu Wah
National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.
Peraro Matteo Dal
Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Di Maio Frank
Department of Biochemistry, University of Washington, Seattle, WA 98195-7370, USA.
Ferrin Thomas E
Department of Pharmaceutical Chemistry and Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158-2517, USA.
Grünewald Kay
Division of Structural Biology, Wellcome Trust Centre of Human Genetics, University of Oxford, OX3 7BN Oxford, UK.
Gutmanas Aleksandras
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Henderson Richard
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Hummer Gerhard
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
Iwasaki Kenji
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Johnson Graham
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158-2330, USA.
Lawson Catherine L
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Meiler Jens
Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA.
Marti-Renom Marc A
Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG) and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08028 Barcelona, Spain.
Montelione Gaetano T
Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Nilges Michael
Département de Biologie Structurale et Chimie, Unité de Bioinformatique Structurale, Institut Pasteur, F-75015 Paris, France; Unité Mixte de Recherche 3258, Centre National de la Recherche Scientifique, F-75015 Paris, France.
Nussinov Ruth
Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
Patwardhan Ardan
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Rappsilber Juri
Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany.
Read Randy J
Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
Saibil Helen
Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.
Schröder Gunnar F
Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
Schwieters Charles D
Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-0520, USA.
Seidel Claus A M
Chair for Molecular Physical Chemistry, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany.
Svergun Dmitri
European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.
Topf Maya
Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.
Ulrich Eldon L
BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.
Velankar Sameer
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Westbrook John D
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
References (75)
75 references, click to expand
  1. Outcome of the first electron microscopy validation task force meeting.
    Structure. 2012 Feb 8;20(2):205-14 PMID: 22325770
  2. Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.
    Structure. 2013 Jun 4;21(6):875-81 PMID: 23747111
  3. The structural dynamics of macromolecular processes.
    Curr Opin Cell Biol. 2009 Feb;21(1):97-108 PMID: 19223165
  4. Inferential structure determination.
    Science. 2005 Jul 8;309(5732):303-6 PMID: 16002620
  5. From words to literature in structural proteomics.
    Nature. 2003 Mar 13;422(6928):216-25 PMID: 12634795
  6. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.
    Mol Cell Proteomics. 2014 Nov;13(11):2927-43 PMID: 25161197
  7. Escape from lysosomes.
    Nat New Biol. 1971 Oct 20;233(42):223 PMID: 20480989
  8. Recommendations of the wwPDB NMR Validation Task Force.
    Structure. 2013 Sep 3;21(9):1563-70 PMID: 24010715
  9. The Protein Model Portal--a comprehensive resource for protein structure and model information.
    Database (Oxford). 2013 Apr 26;2013:bat031 PMID: 23624946
  10. The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.
    J Struct Funct Genomics. 2011 Jul;12(2):45-54 PMID: 21472436
  11. Global rigid body modeling of macromolecular complexes against small-angle scattering data.
    Biophys J. 2005 Aug;89(2):1237-50 PMID: 15923225
  12. A model of the complex between single-stranded DNA and the single-stranded DNA binding protein encoded by gene V of filamentous bacteriophage M13.
    J Mol Biol. 1994 Jul 22;240(4):341-57 PMID: 8035458
  13. Announcing the worldwide Protein Data Bank.
    Nat Struct Biol. 2003 Dec;10(12):980 PMID: 14634627
  14. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.
    Nature. 1953 Apr 25;171(4356):737-8 PMID: 13054692
  15. The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.
    Proteins. 2014 Feb;82 Suppl 2:219-30 PMID: 24327305
  16. Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy.
    Science. 1991 Jun 7;252(5011):1390-9 PMID: 2047852
  17. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.
    EMBO J. 2010 Feb 17;29(4):717-26 PMID: 20094031
  18. Structure and dynamics of full-length HIV-1 capsid protein in solution.
    J Am Chem Soc. 2013 Oct 30;135(43):16133-47 PMID: 24066695
  19. Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy.
    Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9437-42 PMID: 21596998
  20. Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR.
    Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):E445-54 PMID: 24474795
  21. The molecular sociology of the cell.
    Nature. 2007 Dec 13;450(7172):973-82 PMID: 18075576
  22. Consistent blind protein structure generation from NMR chemical shift data.
    Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4685-90 PMID: 18326625
  23. Biochemistry. Integrative structural biology.
    Science. 2013 Feb 22;339(6122):913-5 PMID: 23430643
  24. The protein structure initiative structural genomics knowledgebase.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D365-8 PMID: 19010965
  25. Energy barriers and driving forces in tRNA translocation through the ribosome.
    Nat Struct Mol Biol. 2013 Dec;20(12):1390-6 PMID: 24186064
  26. Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution.
    Acta Crystallogr D Biol Crystallogr. 2012 Jun;68(Pt 6):620-6 PMID: 22683784
  27. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex.
    Cell. 2002 Mar 8;108(5):599-614 PMID: 11893332
  28. The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data.
    J Am Med Inform Assoc. 2014 Nov-Dec;21(6):957-8 PMID: 25008006
  29. A new generation of crystallographic validation tools for the protein data bank.
    Structure. 2011 Oct 12;19(10):1395-412 PMID: 22000512
  30. SASBDB, a repository for biological small-angle scattering data.
    Nucleic Acids Res. 2015 Jan;43(Database issue):D357-63 PMID: 25352555
  31. Outcome of a workshop on archiving structural models of biological macromolecules.
    Structure. 2006 Aug;14(8):1211-7 PMID: 16955948
  32. Atomic model of the type III secretion system needle.
    Nature. 2012 May 20;486(7402):276-9 PMID: 22699623
  33. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.
    Proc Natl Acad Sci U S A. 2000 May 23;97(11):5802-6 PMID: 10811876
  34. Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction.
    Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1379-84 PMID: 24474762
  35. Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.
    Nat Chem Biol. 2013 Oct;9(10):623-9 PMID: 23912165
  36. Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ.
    Structure. 2014 Sep 2;22(9):1239-51 PMID: 25087511
  37. From comparisons of protein sequences and structures to protein modelling and design.
    Trends Biochem Sci. 1990 Jun;15(6):235-40 PMID: 2200167
  38. Structural basis of transcription initiation.
    Science. 2012 Nov 23;338(6110):1076-80 PMID: 23086998
  39. Uncertainty in integrative structural modeling.
    Curr Opin Struct Biol. 2014 Oct;28:96-104 PMID: 25173450
  40. Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering.
    IUCrJ. 2015 Feb 26;2(Pt 2):207-17 PMID: 25866658
  41. Quantitative cross-linking/mass spectrometry using isotope-labelled cross-linkers.
    J Proteomics. 2013 Aug 2;88:120-8 PMID: 23541715
  42. Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling.
    Structure. 2013 Jul 2;21(7):1097-1106 PMID: 23810695
  43. Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.
    Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10873-8 PMID: 22733734
  44. Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex.
    EMBO J. 2014 Nov 3;33(21):2534-46 PMID: 25216679
  45. Comparative protein structure modeling of genes and genomes.
    Annu Rev Biophys Biomol Struct. 2000;29:291-325 PMID: 10940251
  46. Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein.
    Nat Commun. 2011 Oct 11;2:493 PMID: 21988909
  47. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain.
    Proc Natl Acad Sci U S A. 1951 Apr;37(4):205-11 PMID: 14816373
  48. The relative orientation of Gla and EGF domains in coagulation factor X is altered by Ca2+ binding to the first EGF domain. A combined NMR-small angle X-ray scattering study.
    Biochemistry. 1996 Sep 10;35(36):11547-59 PMID: 8794734
  49. Hybrid methods for macromolecular structure determination: experiment with expectations.
    Curr Opin Struct Biol. 2015 Apr;31:20-7 PMID: 25795086
  50. Cardiac myosin-binding protein C decorates F-actin: implications for cardiac function.
    Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18360-5 PMID: 19011110
  51. Structures of fd gene 5 protein.nucleic acid complexes: a combined solution scattering and electron microscopy study.
    J Mol Biol. 1995 Jun 9;249(3):576-94 PMID: 7783213
  52. EMDataBank.org: unified data resource for CryoEM.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D456-64 PMID: 20935055
  53. Conjoined use of EM and NMR in RNA structure refinement.
    PLoS One. 2015 Mar 23;10(3):e0120445 PMID: 25798848
  54. Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein.
    J Mol Biol. 2000 Jun 30;300(1):197-212 PMID: 10864509
  55. Conformational changes during pore formation by the perforin-related protein pleurotolysin.
    PLoS Biol. 2015 Feb 05;13(2):e1002049 PMID: 25654333
  56. Integrating diverse data for structure determination of macromolecular assemblies.
    Annu Rev Biochem. 2008;77:443-77 PMID: 18318657
  57. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.
    Nat Struct Mol Biol. 2011 Jan;18(1):107-14 PMID: 21131981
  58. Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations.
    J Chem Theory Comput. 2014 Jan 14;10(1):423-31 PMID: 26579921
  59. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies.
    PLoS Biol. 2012 Jan;10(1):e1001244 PMID: 22272186
  60. Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography.
    J Mol Biol. 2010 Dec 17;404(5):751-72 PMID: 20933521
  61. A toolkit and benchmark study for FRET-restrained high-precision structural modeling.
    Nat Methods. 2012 Dec;9(12):1218-25 PMID: 23142871
  62. Structure and flexibility within proteins as identified through small angle X-ray scattering.
    Gen Physiol Biophys. 2009 Jun;28(2):174-89 PMID: 19592714
  63. Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly.
    Nat Commun. 2010 Oct 19;1:95 PMID: 20981023
  64. High-speed AFM imaging.
    Curr Opin Struct Biol. 2014 Oct;28:63-8 PMID: 25126765
  65. The Protein Model Portal.
    J Struct Funct Genomics. 2009 Mar;10(1):1-8 PMID: 19037750
  66. Outcome of a workshop on applications of protein models in biomedical research.
    Structure. 2009 Feb 13;17(2):151-9 PMID: 19217386
  67. A mass spectrometry-based hybrid method for structural modeling of protein complexes.
    Nat Methods. 2014 Apr;11(4):403-6 PMID: 24509631
  68. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.
    J Biomol NMR. 2008 Mar;40(3):153-5 PMID: 18288446
  69. A nano-positioning system for macromolecular structural analysis.
    Nat Methods. 2008 Nov;5(11):965-71 PMID: 18849988
  70. Proton-powered subunit rotation in single membrane-bound F0F1-ATP synthase.
    Nat Struct Mol Biol. 2004 Feb;11(2):135-41 PMID: 14730350
  71. Assessing precision and accuracy of protein structures derived from NMR data.
    Proteins. 2005 Jun 1;59(4):655-61 PMID: 15822105
  72. Determining the architectures of macromolecular assemblies.
    Nature. 2007 Nov 29;450(7170):683-94 PMID: 18046405
  73. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.
    Nat Biotechnol. 2011 Dec 25;30(1):90-8 PMID: 22198700
  74. Structure of the actin-myosin complex and its implications for muscle contraction.
    Science. 1993 Jul 2;261(5117):58-65 PMID: 8316858
  75. Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.
    J Mol Biol. 2009 Apr 24;388(1):180-94 PMID: 19233204
Article Info
Journal
Structure (London, England : 1993)
Abbr.
Structure
ISSN
1878-4186
DOI
10.1016/j.str.2015.05.013
Email
sali@salilab.org
Published
2015-07-07
Epub
2015-00-18
Pages
1156-67
Language
English
Region
United States
NLM ID
101087697
PMCID
PMC4933300
Subset
IM
Grants
NLM NIH HHS · P41 LM05799 · United States
NIA NIH HHS · P01 AG002132 · United States
Wellcome Trust · 082961 · United Kingdom
NLM NIH HHS · P41 LM005799 · United States
NIGMS NIH HHS · R01 GM079429 · United States
NIGMS NIH HHS · GM079429 · United States
Wellcome Trust · 103139/Z/13/Z · United Kingdom
Wellcome Trust · 103139 · United Kingdom
NIGMS NIH HHS · U01 GM093324 · United States
Wellcome Trust · 088944 · United Kingdom
Wellcome Trust · 100140 · United Kingdom
Medical Research Council · MC_U105184322 · United Kingdom
External Links
PubMed source DOI: 10.1016/j.str.2015.05.013 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2