Course_June17 21_2024 - I2PC/scipion-courses GitHub Wiki

Model Building

Model Building Agenda

June 17th

• 09:00 - 09:15: Welcome
• 09:15 - 10:15: Introduction to the compute environment to be used in this course (aws/scipion) (P)
• 10:15 - 11:00: General introduction to model building in cryo-EM (M)
  • Example 1: Try to model with Coot
• 11:00 - 11:30: coffee break
• 11:30 - 13:00: Introduction to the data used in the practical sessions (human_haemoglobin) (details here) (M)
  • Review Kahoot students, teacher (R: 000 - Scipion Model building )
  • Homology modeling workflow (r)
  • Import map and sequence. Input data (R)
• 13:00-13:30: Map preprocessing (M)

  TAKE HOME MESSAGE: Try to improve the visual aspect of your map in terms of connectivity and/or details before tracing it.

• 13:30-14:30: Lunch
• 14:30-16:00: Getting a first estimate of the model "de novo" (AlphaFold & ModelAngelo) and by sequence homology. (R-R-M)

  TAKE HOME MESSAGE: Use the structure of an homologous sequence if you have it, otherwise try ModelAngelo if your map's resolution is good enough, alternatively try to predict the structure with AlphaFold.

• 16:00-16:30: Coffee break
• 16:30-17:00: Continue with previous task.
• 17:00-17:30: Structure analysis: Structure comparison (M)

  TAKE HOME MESSAGE: Models are always wrong... but some are useful.

• 17:30-18:00: Rigid Fitting of Initial Models (R)
• 18:00: End of the day

June 18th

• 09:00-09:30: Review yesterday's work (R)

• 09:30-11:00: Flexible fitting (Coot) and Validation

  • Coot Tutorial (R)

• 11:00-11:30: Coffee break

• 11:30-13:30: Flexible fitting (Phenix & Refmac) and Validation (M-M)

• 13:30-14:30: Lunch

• 14:30-15:00: Review Kahoot students, teacher (R: 0001 - revision)

• 15:00-16:00: Model building of human Hgb beta subunit (R-M)

• 16:00-16:30: Coffee break

• 16:30-17:00 Building the model of the whole protein

  • Chain merge & symmetrization (R)

• 17:00-17:30: Submission of structures to EMDB. Understanding the validation report. Haemoglobin PDB full validation report (R)

  • Comparison validation scores PDB structure(M)

• 17:30: Structure analysis: chain contacts Structural search with DALI Structural search with FOLDSEEK (M)

• 18:30:End of the day

• XX:XX: * Review Kahoot students, teacher (R: Review Model Building)

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Course Material

• Presentations

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

• Practical working sessions:

  1. Homology modeling workflow
  2. AlphaFold & ModelAngelo modeling workflow

Data resources and IDs

• How to access to the remote desktop

• 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)