I2PC INSTRUCT course: INTRODUCTION TO MODEL BUILDING 2022 - I2PC/scipion-courses GitHub Wiki

Model Building Course Material

• Presentation

  • Introduction to Model Building presentation
  • Introduction to AlphaFold2
  • Scipion model building tutorials:
    1. Model building by Homology
    2. Build initial model with AlphaFold
  • Specimens:
    1. Human haemoglobin
    2. Human ion channel-like protein TACAN

• Practical working sessions:

  1. Homology modeling workflow
  2. AlphaFold modeling workflow

Agenda

• June 22nd

1. How to access to the remote desktop
2. Importing data in Scipion
3. Prediction of atomic structures with AlphaFold2 + Processing
4. Map Preprocessing
5. Model prediction by sequence homology
6. Afternoon task proposal 1

• June 23rd

1. Review (Kahoot)
2. Rigid Fitting of Initial Models
3. Flexible fitting
4. Validation
5. Afternoon task proposal 2

• June 24th

1. Review
2. Summary (Kahoot)
3. Chain merge & symmetrization
4. Analysis: contacts
5. Comparison validation scores PDB structure
6. Submission
7. Summary

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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)

• Human ion channel-like protein TACAN

  • 3D map: emd-31482.map, available directory Data
  • sequence:
    • UniProt ID Q9BXJ8

• 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