IHM Meeting Summary Nov 16 2017

Integrative/Hybrid (I/H) methods meeting, Thursday November 16th, 2017

We organized a "large" I/H methods virtual meeting with representatives from the I/H methods task force members and the wwPDB partners. Eleven 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)                     sali[at]salilab.org
Torsten Schwede (SIB, Switzerland)          torsten.schwede[at]unibas.ch
Gerhard Hummer (MPI, Germany)               gerhard.hummer[at]biophys.mpg.de
Jens Meiler (Vanderbilt, USA)               jens.meiler[at]vanderbilt.edu
Frank DiMaio (U. Washington, USA)           dimaio[at]u.washington.edu
Emad Tajkhorshid (UIUC, USA)                emad[at]life.illinois.edu
Alexandre Bonvin (Utrecht U, Netherlands)   a.m.j.j.bonvin[at]uu.nl

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)           martirenom[at]cnag.crg.eu
Oliver Brock (Technische U, Germany)     oliver.brock[at]tu-berlin.de

Meeting Attendees (representatives from the above groups)

Ben Webb (UCSF, USA)                    ben[at]salilab.org
Tom Goddard (RBVI, USA)                 goddard[at]cgl.ucsf.edu
John Westbrook (RCSB PDB, USA)          john.westbrook[at]rcsb.org
Brinda Vallat (RCSB, USA)               brinda.vallat[at]rcsb.org
Aleksandras Gutmanas (PDBe, UK)         gutmanas[at]ebi.ac.uk
John Berrisford (PDBe, UK)              jmb[at]ebi.ac.uk
Mike Goodstadt (CNAG, Spain)            mike.goodstadt[at]cnag.crg.eu
Hirofumi Suzuki (PDBj, Japan)           hirofumi[at]protein.osaka-u.ac.jp
Gert-Jan Bekker (PDBj, Japan)           gertjan.bekker[at]protein.osaka-u.ac.jp
Kumaran Baskaran (BMRB, USA)            kbaskaran2[at]wisc.edu
Lukas Honig (Technische U, Germany)     l.hoenig[at]campus.tu-berlin.de

Meeting Agenda

1. Update on I/H methods project
2. Open discussion

Meeting Summary

1. Brinda Vallat provided an update on the I/H methods project.

   • PDB-Dev announcement published is Structure (Burley SK, et al. Structure. 2017 Sep 5; 25(9):1317-1318. doi: 10.1016/j.str.2017.08.001.
   • The dictionary paper is under preparation and grant proposals are under review.
   • Eight structures in PDB-Dev
     • Nup84, exosome, mediator
     • Chromosome 2L domain from Drosophila Melanogaster
     • Diubiquitin, human serum albumin domains
     • One new entry is under process
   • PDB-Dev now provides accession codes
   • Dictionary updates include the following:
     • Hierarchical structural assemblies
     • Predicted contacts from high-throughput sequencing experiments
     • Extensions to handle atomic I/H models
     • Dictionary is now available on the PDBx/mmCIF resource site
     • Dictionary extensions to be addressed in the near future include:
       • Issue 47: Generic distance information class
       • Issue 46: Interface mapping information
   • IMP code for generating dictionary compliant data file is available here.
   • ChimeraX can visualize atomic I/H models.
   • Dictionary and documentation are available on the project GitHub site.
   • Visit the GitHub issues page for active issues.
   • Visit the GitHub wiki page for meeting summaries.
   • Current focus is on getting more structures in PDB-Dev.

2. Open discussion focused on the following:

   • The rate-limiting step in obtaining more structures is getting them in a dictionary compliant format. IMP has internal support to output files that are compliant with the dictionary. IMP code for writing mmCIF files is open source and can be used by anyone. Although the script supports writing mmCIF files, the alignment of the internal IMP data model to the dictionary data model is a challenge. HADDOCK and Rosetta developers are working on adding similar support in their software to produce dictionary compliant files.
   • HADDOCK is agnostic to the source of distance restraints. A generic distance restraint class is required (Issue 47) and will be addressed in the next dictionary update. A similar approach was used while developing the NEF dictionary. The specific restraint categories currently defined in the I/H methods dictionary were created based on the examples available at the time.
   • PDB-Dev depUI is a simple file upload interface. Processing time for an entry usually involves contacting the author to fill-in missing information in the data file. Current validation involves checking for compliance with the dictionary. The wwPDB I/H methods task force model validation sub-group members are addressing the requirements for developing methods for model validation.
   • wwPDB policy regarding I/H structures is available here. This provides a general set of guidelines regarding which structures belong to the PDB and PDB-Dev. Initially, decisions may need to be made on a case-by-case basis. It may be useful for Brinda and Ben to attend one of the upcoming OneDep meetings for further discussion.
   • Submissions to PDB-Dev require at least one set of restraints derived from experiments carried out on a physical sample. Purely in silico models are archived in the Model Archive. Structures that are predominantly determined from X-ray, NMR or EM experiments, combined with restraints from other biophysical experiments (example: NMR+SAS) are archived in the PDB.
   • Future ChimeraX developments will incorporate support for writing dictionary compliant data files. Visualization of I/H structures on ChimeraX requires downloading the daily build of the software and using "format ihm" as a command line option (or the file extension of the data file can be changed to *.ihm instead of *.cif).
   • There was an extensive discussion on Issue 3 regarding the use of a different file extension for I/H structures. Feedback from the 4D genome community may be helpful.
   • At least two structures have been deposited by research groups that are not part of the I/H methods task force. These are from researchers who have either seen the announcement paper in Structure or have attended conferences where PDB-dev was presented. At a recent 4D genome conference, PDB-Dev was introduced and was received with great interest.