Instruct course on flexibility analysis and integrative modelling using Scipion. Madrid, June 17 – 21, 2024

Venue

Madrid’s Institute for Material Sciences (ICMM-CSIC), Madrid, Spain
Madrid, June 17 – 21, 2024
How to find us: Contact | ICMM (csic.es)

Overall aims and course outline

Cryo-Electron Microscopy has established itself as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and is capable of accessing the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like the PDB.
The aim of the course is to introduce attendees to two techniques that are normally needed at the end of the Cryo-Electron Microscopy image processing pipeline: 1) understanding the possible continuous heterogeneity/flexibility of the sample, helping to obtain dynamical information in the form of conformational landscapes, and 2) interpreting the reconstructed map by means of an atomic model. The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand.
We will use our software platform Scipion to present these two topics. Scipion is an integrative platform that allows interoperability among different software packages. In the domain of flexibility analysis, we include our own developments in Xmipp as well as tools coming from CryoDrgn, ProDy and HEMNMA. For the atomic modelling part, we include software like Coot, Chimera, Refmac, Phenix, and AlphaFold. In addition to simplifying the access to all these software packages in an integrated manner, Scipion adds a traceability and reproducibility layer so that any other researcher can understand the modelling workflow followed to reach a particular model.
This course is addressed to investigators at all levels.

Motivation for the I2PC course on conformational and compositional heterogeneity:
We want this course to help researchers to get introduced in the area of flexibility/heterogeneity analysis, one of the most advanced topics in SPA. For some of the most used methods in the field (some developed by us, some by others) we will
present the theory behind the method and perform a short practical. We will do so within the integrative Scipion Flexibility Hub environment, to help in the use of these multiple methods.

Expected impact for young researchers

Atomic modelling of the CryoEM map is currently at the moment the natural next step once the map is reconstructed. Flexibility analysis is currently not so common, but the advantage of CryoEM is that it can capture the different conformations of the macromolecules under study. Both techniques are valuable assets in young researchers already with a background on image processing in CryoEM.

Contacts

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

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

Tutors

Marta Martinez (MM) – Modelling specialist @BCU/i2PC
Roberto Marabini (RM) – Professor @UAM, Collaborator @BCU/i2PC
Carlos P. Mata (CM) – Single Particle Analysis specialist @BCU/i2pc
Marcos Gragera(MG) – Single Particle Analysis specialist @BCU/i2pc
David Herreros (DH) – Flexibility Hub head developer @BCU
James Krieger (JK) – Flexibility Analysis specialist @ BCU/i2PC
Carlos-Oscar Sorzano (COS) – Group leader @ BCU, Technical Director @ i2PC

Registration Fee

  • Academic Registration Fee Instruct countries: Predocs & Postdosc 50€
  • Academic Registration Fee Instruct countries: Others 100€
  • Academic Registration Fee Non Instruct countries: Predocs & Postdosc 100€
  • Academic Registration Fee Non Instruct countries: Others 150€
  • Industrial Registration Fee 300€

You can fill your registration here

Agenda

 Times are expressed in CET time Zone

DAY 1: Modeling

09:00-09:15 Welcome
09:15 – 10:15: Introduction to the compute environment to be used in this course (aws/scipion)
10:15 – 11:00:General introduction to model building in cryo-EM
11:00 – 11:30: Coffee break
11:30 – 13:00: Introduction to the data used in the practical session in homology modeling (details here) and de novo modeling
13:00-13:30: Map preprocessing I
13:30-14:30: Lunch break
14:30-16:00: Getting a first estimate of the model “de novo” (AlphaFold & ModelAngelo) and by sequence homology. 
16:00-16:30: Coffee break
16:30-17:00: Continuation of first estimation
17:00-17:30: Structure analysis: Structure comparison
17:30-18:00: Rigid Fitting of Initial Models
18:00: End of the day

DAY 2: Modelling

09:00-09:30: Review yesterday’s work 
09:30-11:00: Flexible fitting (Coot) and Validation
11:00-11:30: Coffee break
11:30-13:30: Flexible fitting and Validation
13:30-14:30: Lunch break
14:30-15:00: Review Kahoot students, teacher
15:00-16:00: Coffee break
16:30-17:00 Building the model of the whole protein
Chain merge & symmetrization
17:00-17:30: Submission of structures to EMDB. Understanding the validation report. Haemoglobin PDB full validation report 
Comparison validation scores PDB structure
17:30: Structure analysis: chain contacts Structural search
18:30:End of the day

DAY 3: Flexibility

9:30 – 10:00: Introduction to macromolecular flexibility and Flexibility Hub
10:00 – 10:15: Presentation of the dataset and workflows of the day (Zernike3D – HetSIREN)
10:15 – 11:00: Zernike3Deep (Theory)
11:00 – 11:30: Coffee break
11:30 – 12:30: Zernike3Deep (Practice)
12:30 – 13:00: HetSIREN (Theory)
13:00 – 14:00: Lunch break
14:00 – 15:00: HetSIREN (Practice)
15:00 – 15:30: Dimensionality reduction of estimated landscapes
15:30 – 16:00: Landscape exploration: interactive tools
16:00 – 16:30: Coffee break
16:00 – 17:00: Landscape exploration: interactive tools
17:00 – 17:30: End of the day

DAY 4: Flexibility

9:30 – 10:00: Review from the previous day
10:00 – 10:15: Presentation of the workflows of the day (FlexConsensus – ZART – CryoDRGN)
10:15 – 11:00: Should we trust our conformational landscapes? FlexConsensus (Theory)
11:00 – 11:30: Should we trust our conformational landscapes? FlexConsensus (Practice)
11:30 – 12:00: Coffee break
12:00 – 12:30: Should we trust our conformational landscapes? FlexConsensus (Practice)
12:30 – 13:00: Beyond motion blurr: ZART and flexible refinement (Theory)
13:00 – 14:00: Lunch break
14:00 – 15:00: Beyond motion blurr: ZART and flexible refinement (Practice)
15:00 – 15:30: CryoDRGN (Theory)
15:30 – 16:00: CryoDRGN (Practice)
16:00 – 16:30: Coffee break
16:30 – 17:00: CryoDRGN (Practice)
17:00 – 17:30: Landscape exploration: interactive tools
17:30 – 18:00: End of the day

DAY 5: Flexibility

9:30 – 9:45: Review from the previous day
9:45 – 10:00: Presentation of the workflows of the day (ContinuousFlex – 3DVA – 3DFlex – Prody)
10:00 – 11:00: ContinuousFlex
11:00 – 11:30: Coffee break
11:30 – 12:00: 3DVA (Theory)
12:00 – 13:00: 3DVA (Practice)
13:00 – 14:00: Lunch break
14:00 – 14:30: 3DFlex (Theory)
14:30 – 15:30: 3DFlex (Practice)
15:30 – 16:00: Prody
16:00 – 16:30: Coffee break
16:00 – 17:00: Prody
17:00 – 17:30: End of the day (closing remarks)