I2PC INSTRUCT course: INTRODUCTION TO MODEL BUILDING 2021 - I2PC/scipion-courses GitHub Wiki

Model Building Course Material

• Presentation

  • PPT presentation (model building)
  • Scipion model building tutorial

• Practical working sessions (General modeling workflow)

  1. Review (Kahoot)
  2. Map Preprocessing
  3. From sequence to Model
  4. Rigid Fitting
  5. Flexible fitting - validation
  6. Chain merge & symmetrization
  7. Analysis: contacts

• Data resources and IDs

  • BlastP (search for homologues)
  • Human haemoglobin
    • 3D map: emd_3488.map, available directory Data
    • sequence:
      • alpha subunit: UniProt ID P69905 (Homologous sequences: P01958, P01948, P81023, P83134)
      • beta subunit: UniProt ID P68871 (Homologous sequences: P02062, P02057, G1U9Q8, P83133)
    • PDB reference: 1pbx (antartic fish: Pagothenia bernacchii)

• Coot Tutorial

  • 3D map
  • atomic model

• ChimeraX Tutorial

• EMDB submission link

  • Haemoglobin in PDB: ID 5ni1
    • Haemoglobin PDB full validation report

• Contacts AD type V (Zhou)

Model Building Agenda