Venue
National Center for Biotechnology (CNB), Madrid, Spain
Madrid, June 19 – 23, 2023
How to find us: https://i2pc.es/contact-us/
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.
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
I2PC staff: David Herreros (DH), James Krieger (JK), Marcos Gragera (MG), Marta Martínez (MM), Roberto Marabini (RM), Daniel del Hoyo (DDH)
CNRS IMPMC-CNRS UMR 7590. Sorbonne Université: Remi Vuillemot (RV)
You can fill your registration here (Online registration closed)
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€
| Program |
| Day 1: June 19, 2023 09:30: Introduction to Scipion and AWS 10:15: Introduction to macromolecular flexibility and Flexibility Hub 10:30: Flexibility approaches (theory): – Deformation field-based approach – Density-based approach 11:00: Coffee break 11:30: Presentation of the dataset to be used during the practical session 11:45: Estimation of conformational landscapes 12:45: Flexibility consensus (theory) 13:30: Lunch 14:30: Flexibility consensus (practice) 15:15: Dimensionality reduction of estimated landscapes 16:00: Coffee break 16:30: Conformational landscape analysis tools – Interactive landscape clustering and real-time inspection of conformations – Best number of clusters analysis 18:00 – 18:30: End of the day |
| Day 2 June 20, 2023 09:30: Review from the previous day 09:45: Conformational landscape analysis tools (continuation) – Interactive landscape annotation and real-time inspection of conformations (2D-based tools) 11:00: Coffee break 11:30: Conformational landscape analysis tools (continuation) – Interactive landscape annotation and real-time inspection of conformations (3D-based and hybrid tools) 13:30: Lunch 14:30: Extracting conformational states from landscape selections: Application of deformation fields to maps and structural models + strain/rotation analysis + motion statistics 15:00: Interactive local analysis of motions 15:30: Heterogeneity correction with ZART (theory) 16:00: Coffee break 16:30: Heterogeneity correction with ZART (practice) 17:15: Heterogeneity correction of different landscapes states with ZART 18:00 – 18:30: End of the day |
| Day 3 June 21, 2023 09:00: Review from the previous day 9:45: Introduction to atomic structure ensemble analysis, normal mode analysis, and ProDy 10:15: Ensemble analysis with ProDy ensemble construction, PCA and landscape projection, and motion analysis with NMWiz 11:00: Coffee break 11:30: Conformational landscapes from normal modes and molecular dynamics using ContinuousFlex (theory and practice) 13:30: Lunch 14:30: Introduction to model building in cryo-EM – How to get a first estimation of the model (homology, alphafold, modelangelo) 15:15: Presentation of the data used in the practical session – Kahoot 15:45 min: Map preprocessing – I 16:00: coffee break 16:30: Map preprocessing – II 17:00 : Getting a first estimate of the model 18:00-30: End of the day |
| Day 4 June 22, 2023 09:30 Structure analysis: Structure comparison 10:15: Rigid fitting of initial models 11:00: Coffee Break 11:30: Flexible fitting (coot) and validation (phenix) 13:30: lunch 14:30: Flexible fitting (coot) and validation (phenix) (cont) 15:30: kahoot 16:00: coffee break 16:30: Model building of the Beta sub-unit 18:00-30: end of the day |
| Day 5 June 23, 2023 09:30: Presentation of the course questionnaire 09:45: Building the model of the protein complex 10:30: kahoot. 11:00: Coffee Break 11:30: Submission of structures to EMDB. Understanding the validation report. 12:00: Structure analysis: Chain contacts 13:00: INSTRUCT short message and farewell 13:30: lunch and end of the day |
Fill your registration here (Online registration closed)
This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe.
