IHM Meeting Summary May 24 2018

Integrative/Hybrid (I/H) methods meeting, Thursday May 24th, 2018

We organized a "large" I/H methods virtual meeting with representatives from the I/H methods task force members and the wwPDB partners. Ten 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

Meeting Attendees (representatives from the above groups)

Ben Webb (UCSF, USA)                    ben[at]salilab.org
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
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
Juergen Koefinger (MPI, Germany)        juergen.koefinger[at]biophys.mpg.de 
Mikael Trellet (Utrecht U, Netherlands) m.e.trellet[at]uu.nl
David Castillo Andreo (CNAG, Spain)     [email protected]

Meeting Agenda

1. Update on the IHM-dictionary and PDB-Dev
2. Update on the Python-IHM library
3. Open discussion

Meeting Summary

1. Brinda Vallat provided an update on the IHM-dictionary and PDB-Dev.

   • Paper accepted for publication in Structure (Vallat B et al., Structure. 2018, in press. doi: 10.1016/j.str.2018.03.011).
   • PDB-Dev has structures that come from different modeling software and use restraints derived from diverse experimental methods.
   • The NPC structure published recently in Nature contains PDB-Dev accession codes.
   • The development of the IHM-dictionary is an ongoing process and gets updated with new depositions and new requirements (generic distance restraints for HADDOCK AIR restraints, restraints to geometric objects for the NPC structure).
   • For more details, download the presentation.

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

   • The library provides a mechanism to programmatically generate IHM data files compliant with the IHM-dictionary.
   • The library is an outcome of incorporating automated support for the IHM-dictionary in IMP.
   • The library is IMP-independent and open source.
   • The library is pure python and represents and an IHM system as a set of python classes.
   • For more details, download the presentation.

3. Open discussion focused on the following:

   • Specific structures in PDB-Dev (NPC, Chromosome segment from Fruit Fly, 16sRNA-Methyltransferase A, Mitochondrial Cysteine desulferase
   • Naming conventions and hierarchy in the Python-IHM library
   • Discussion regarding the usage of the Python-IHM library. There was enthusiastic response regarding using the library within other modeling applications in order to support the IHM-dictionary.