Course_June19 23_2023 - I2PC/scipion-courses GitHub Wiki

Flexibility

Model Building

Model Building Agenda

June 21st

• 14:30: General introduction to model building in cryo-EM (M)
• 15:15: Introduction to the data used in the practical session in homology modeling (details here) and de novo modeling (M)
  • Review Kahoot students, teacher (R)
  • Homology modeling workflow (r)
  • Import map and sequence. Input data (R)
• 15:45: Map preprocessing I (M)
  • 16:00: Coffee break
• 16:30: Map preprocessing II (M)

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

• 17:00: 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.

• 18:30: End of the day

June 22nd

• 09:30: Structure analysis: Structure comparison (M)

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

• 10:15: Rigid Fitting of Initial Models (R)
  • 11:00: Coffee break
• 11:30: Flexible fitting (Coot) and Validation
  • Coot Tutorial (R)
  • 13:30: Lunch
• 14:30: Flexible fitting (Phenix & Refmac) and Validation (M-M)
• 15:30: Review Kahoot students, teacher (R)
  • 16:00: Coffee break
• 16:30: Model building of human Hgb beta subunit (R-M)
• 18:30:End of the day

June 23rd

• 09:30: Presentation of course questionnaire

• 09:45: Building the model of the whole protein

  • Chain merge & symmetrization (R)

• 10:30: * Review Kahoot students, teacher (R)

  • 11:00: Coffee break

• 11:30: Submission of structures to EMDB. Understanding the validation report. Haemoglobin PDB full validation report (M)

  • Comparison validation scores PDB structure

• 12:00: Structure analysis: chain contacts M

• 12:30: Structural search

• 13:00: Lunch and end of the day

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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)