Data hierarchy and groupings

Tom Goddard
August 29, 2016

Levels of organization in molecular assemblies. What user interface and data representation are needed?

Examples

• CRISPR: 5cd4. Two copies of complex in crystal asymmetric unit, defined in mmcif assembly table. 6 copies of CasC, 2 copies of CasB, 1 copy of CasA, CasD, CasE. (Identical sequences)
  
• Ribosome 4v6w, 80 protein chains, 6 nucleic acid chains. Large and small subunits not defined in mmCIF.
  
• Nuclear pore, about 20 nucleoporin proteins with 11 x-ray structure complexes (5HAX 5HAY 5HAZ 5HB0 5HB1 5HB2 5HB3 5HB4 5HB5 5HB6 5HB7 5HB8) fit into cryoEM map (3103). Journal article, April 2016 Science. Architecture of the symmetric core of the nuclear pore. Hoelz lab web page with more images. 8-fold symmetry. How would you find all contacts between 2 of 8 spokes, or between channel and adaptor proteins?