I2PC – INSTRUCT COURSE: INTRODUCTION TO MODEL BUILDING

Venue

Remote course
June 22th to June 24th (2022) (3 days):
*3 Mornings: Presentations and training.
*2 Afternoons: Personal work.

Aim of the course:

Hands-On Training Course that introduces the  fundamentals and main tools needed to build an atomic model in the context of cryo-EM, starting from a 3D map and the aminoacid sequence of each protein chain. The  tools will be used inside the Scipion framework (de la Rosa-Trevin et al. 2016) and examples will focus on the modeling by homology scenario, including AlphaFold2 prediction models.

Expected impact for young researchers

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. In this course, we introduce the basic tools needed to perform this task. Ph.D. students, as well as post-docs, will undoubtedly benefit from approaching this technique since atomic models guide our mechanistic interpretation of cryo-EM structures.

Contacts

Lead contact:  
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

Marta Martínez (MM), Roberto Marabini (RM)

Schedule and contents:

*June 22th:

  • 9:30: Welcome and presentation of the course, dynamics and mentors.
  • 10:00: Introduction to model building in the context of cryo-EM and Scipion
  • 10:30: Introduction to Scipion (import data)and AWS
  • 11:30: Map preprocessing
  • 12:00: Break
  • 12:15: Introduction to AlphaFold2 (Searching for prediction models)
  • 13:00: Searching models by homology
  • 13:30: Afternoon task proposal

*June 23th:

  • 9:30: Review of contents and follow up of the afternoon task proposal.
  • 10:00: Kahoot
  • 10:15: Rigid fitting of initial models
  • 11:00: Flexible fitting
  • 12:00: Break
  • 12:15: Flexible fitting (continuation)
  •  14:00: Afternoon task proposal

*June 24th:

  • 9:30: Review of contents and follow up of the afternoon task proposal.
  • 9:45: Presentation of the course questionnaire
  • 10:00: Kahoot
  • 10:15: Assessment and validation of models
  • 11: 00: Building the model of the protein complex
  • 11:15: Break
  • 11:30: Structure analysis: Chain contacts
  • 12:00: Structure analysis: Structure comparison
  • 12:30: Submission of structures
  • 13:00: Summary
  • 13:30: INSTRUCT short message and farewell

REGISTRATION

Registration Fee: 50€ 
Fill  your application here

This course is organized by I2PC in collaboration with Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and CRIOMECORR Project