2017-10-18 : 5247 EMDB map entries, 1838 PDB coordinate entries PDBe | RCSB    

One-stop shop for 3DEM deposition and retrieval

fitted em map density

Modelling of CryoEM Maps Workshop

You have a brand-new cryoEM density map of a biological assembly and want to generate a realistic coordinate model that fits the density. How should you proceed? This was the primary topic of discussion at the Modelling of CryoEM maps workshop held at the University of Houston on January 14-18, 2010. Approximately 95 participants spent mornings listening to lectures and afternoons following instructor-guided tutorials. Possible approaches that were described include:

  • detecting secondary structure elements (SSEhunter)
  • building models directly into maps (Gorgon)
  • building de novo models from primary sequence guided by the map (Rosetta)
  • combining multiple structural data types to generate a model (IMP)
  • molecular dynamics flexible fitting (MDFF)
  • conformational sampling under low resolution restraints (Direx)

In addition, Helen Berman (RCSB-PDB) provided an introduction to EMDB (map) and PDB (coordinate model) archives, Gerard Kleywegt (PDBe) explained why model validation has become integral to the X-ray crystallography method, and Cathy Lawson (RCSB-PDB) ran a tutorial on EM map+model deposition and retrieval, which included a new map+model deposition guide, available here.  You can download workshop presentations from this page.