Alexei Adzhubei

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Topic 4

• Alexei Adzhubei

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Current public, searchable databases with
protein models as primary data content

• RSCB PDB
• has a subset of model data (excluded from the
  main archive) http//www.rcsb.org/pdb/cgi/models.c
  gi
• SwissModel Repository
• SwissModel automated homology-modelling
  http//swissmodel.expasy.org/repository/
• MODBASE
• models generated automatically by MODELLER
  http//modbase.compbio.ucsf.edu/
• MDB
• models from PDB, compatible with PDB, built using
  the MDB dictionary (mmCIF and PDBML)
  http//sgp.uio.no/mdb/
• PMD
• CASP models http//a.caspur.it/PMDB/
• ?

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How to store and access models?

• Create a central repository?
• Create a network of databases?
• Major questions
• what models to store (automatic, expert)
• what primary data to store
• what generated data to store (e.g. model
  accuracy) and how to generate it
• what data to distribute to participating
  databases in a network of databases

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Things to do

• Develop a Model data description standard
  acceptable for everyone
• Develop data exchange format based on either
  mmCIF, PDBML or other and use it for data
  exchange between databases and servers
• Develop a Minimal Data standard for data
  exchange