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IHM Meeting Summary Sep 13 2018

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brindakv edited this page Sep 14, 2018 · 1 revision

Integrative/Hybrid (I/H) methods meeting, Thursday Sep 13th, 2018

We organized a "large" I/H methods virtual meeting with representatives from the I/H methods task force members and the wwPDB partners. Nine participants from various groups attended the meeting. Meeting invites were sent to representatives from the following groups and the meeting time was decided based on a Doodle poll.

wwPDB I/H methods task force members

Andrej Sali (UCSF, USA)             
Torsten Schwede (SIB, Switzerland) 
Gerhard Hummer (MPI, Germany)      
Jens Meiler (Vanderbilt, USA)     
Frank DiMaio (U. Washington, USA) 
Emad Tajkhorshid (UIUC, USA)      
Alexandre Bonvin (Utrecht U, Netherlands)

ChimeraX developers

RBVI (UCSF, USA)

wwPDB partners

RCSB PDB (Rutgers, USA)

PDBe (EBI, UK)

PDBj (Osaka U, Japan)

BMRB (U. Wisconsin)

Research groups working on I/H modeling

Marc Marti-Renom (CNAG, Spain)

Meeting Attendees (representatives from the above groups)

Ben Webb (UCSF, USA)                    
Tom Goddard (RBVI, UCSF, USA)
John Westbrook (RCSB PDB, USA)          
Brinda Vallat (RCSB, USA)               
Aleksandras Gutmanas (PDBe, UK)         
John Berrisford (PDBe, UK)           
Kumaran Baskaran (BMRB, USA)            
Juergen Haas (SIB, Switzerland)         
Mikael Trellet (Utrecht U, Netherlands) 
Brian Jimenez (Utrecht U, Netherlands)

Meeting Agenda

  1. Update on current structures in PDB-Dev
  2. Update on the IHM-dictionary, MA-dictionary and the FLR-dictionary
  3. Update on the Python-IHM library
  4. Support for the IHM-dictionary in HADDOCK
  5. Open discussion

Meeting Summary

  1. Brinda Vallat provided an update on the structure in PDB-Dev and other data dictionaries.

    • Basic statistics about the different kinds of I/H structures in PDB-Dev and the types of experimental restraints and modeling software used
    • IHM-dictionary contains distance restraints to geometric features
    • FLR-dictionary to represent Fluorescent experiments
    • MA-dictionary to describe computational models
    • Incorrect depositions on PDB-Dev (about 70 X-ray/EM structures, 5 theoretical models)
    • Emails have been sent to the depositors about redepositing their structures in the correct place
    • Integrative structure determination federation (iSDF) workshop to be organized in the spring of 2019. May be held as a satellite meeting at the 2019 Biophysical society meeting
    • For more details, download the presentation

  2. Ben Webb provided an update of the new Python-IHM library.

  3. Mikael Trellet provided an overview for developing support for the IHM-dictionary within HADDOCK

    • Current support for reading/writing coordinates
    • Work is in progress to provide support for other metadata including experimental restraints
    • Yet to evaluate the feasibility of using PDBx/mmCIF as internal format
    • Current support is based on the Python-IHM library
    • For more details, download the presentation

  4. Open discussion focused on the following:

    • Policy regarding which structures belong to PDB-Dev; how much experimental data is required so that a structure can be archived in PDB-Dev? These issues will need to be addressed by the community, perhaps in the upcoming iSDF workshop.
    • How to handle incorrect depositions? Provide clear information on the PDB-Dev deposition page regarding which structures belong to which repository
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