Hybrid/Integrative Methods Task Force

The wwPDB established a wwPDB Hybrid Methods Task Force composed of experts in the various experimental fields that are contributing to these hybrid studies, experts in hybrid modeling, and experts in archiving. The first meeting was held October 6-7, 2014 at EMBL-EBI (Hinxton, UK) to discuss the many issues involved in archiving models determined by hybrid methods.

The white paper from this meeting has been published: Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop Structure 23: 1156-1167 doi:  10.1016/j.str.2015.05.013.

Task Force recommendation for integrative structures currently on-hold awaiting a policy decision (status code POLC).

I/HM Deposition

Deposit I/HM Structures to PDB-IHM

PDB-Dev: A prototype system for depositing integrative/hybrid structural models. Structure 25: 1317-1318 doi: 10.1016/j.str.2017.08.001

2019 Workshop

In 2019, a Workshop was held as a Biophysical Society (BPS) Satellite Meeting to assess progress regarding the implementation of Task Force recommendations and to discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The workshop was attended by experts in various experimental methods, integrative modelers and wwPDB members.

The summary of the workshop and the recommendations that emerged have been published in a white paper: Structure 27: 1745-1759 doi: 10.1016/j.str.2019.11.002

2014 Workshop Participants:

Paul Adams (Lawrence Berkeley National Laboratory), Alexandre Bonvin (Utrecht University), Wah Chiu (Baylor), Matteo dal Peraro (École Polytechnique Fédérale de Lausanne), Frank Di Maio (University of Washington), Tom Ferrin (University of California, San Francisco), Kay Grünewald (University of Oxford), Richard Henderson (MRC Laboratory of Molecular Biology), Gerhard Hummer (The Max Planck Institute of Biophysics), Kenji Iwasaki (Osaka University), Graham Johnson (University of California, San Francisco), Marc Marti-Renom (Centre for Genomic Regulation), Jens Meiler (Vanderbilt University), Guy Montelione (Rutgers), Michael Nilges (Institut Pasteur), Ruth Nussinov (Tel Aviv University), Juri Rappsilber (University of Edinburgh), Randy Read (Cambridge University), Helen Saibil (University of London), Andrej Sali (University of California, San Francisco), Gunnar Schröder (Forschungszentrum Jülich), Torsten Schwede (University of Basel), Charles Schwieters (National Institute of Health), Claus Seidel (Heinrich-Heine University), Dimtri Svergun (EMBL Hamburg), Maya Topf (Birkbeck University of London), Jill Trewhella (University of Sydney)
wwPDB and EMDataBank Representatives: Helen Berman (RCSB PDB), Stephen Burley (RCSB PDB), Aleksandras Gutmanas (PDBe), Gerard Kleywegt (PDBe), Cathy Lawson (RCSB PDB), John Markley (BMRB), Haruki Nakamura (PDBj), Ardan Patwardhan (PDBe), Eldon Ulrich (BMRB), Sameer Velankar (PDBe), John Westbrook (RCSB PDB)

2019 Workshop participants

Paul D. Adams, Helen M. Berman, Alexandre A. Bonvin, Stephen K. Burley, Bridget Carragher, Wah Chiu, Frank DiMaio, Thomas E. Ferrin, Margaret J. Gabanyi, Thomas D. Goddard, Patrick R. Griffin, Juergen Haas, Christian A. Hanke, Jeffrey C. Hoch, Gerhard Hummer, Genji Kurisu, Catherine L. Lawson, Alexander Leitner, John L. Markley, Jens Meiler, Gaetano T. Montelione, George N. Phillips, Jr., Thomas Prisner, Juri Rappsilber, Andrej Sali, David C. Schriemer, Torsten Schwede, Claus A.M. Seidel, Timothy S. Strutzenberg, Dmitri I. Svergun, Emad Tajkhorshid, Jill Trewhella, Brinda Vallat, Sameer Velankar, Geerten W. Vuister, Benjamin Webb, John D. Westbrook, Kate L. White