WINTER SCHOOL ALGORITHMS
IN STRUCTURAL BIOINFORMATICS :

MODELING LARGE MACROMOLECULAR ASSEMBLIES

8-12 december 2014, Inria Sophia Antipolis, France

• Home
• Lectures
• Practicals
• Venue
• Registration
• Accommodation
• Organizers
• Previous editions

 

[Daily Schedule]

• Morning session: lecture from 9am to noon.
• Afternoon session: practical from 2pm to 5pm.

[Monday the 8th] Modeling of Dynamic Biomolecular Assemblies

Instructor: Gerhard Hummer , Max Plack Institut fur Biophysik / Theoretical Biophysics

Slides:

Topics: Coarse-grained representation of protein-protein interactions. Sampling of conformational dynamics in supramolecular assemblies. Hybrid structural modeling through combination of simulation and experiment. Ensemble refinement.

 

[Tuesday the 9th] Small Angle X-ray Scattering from Macromolecular Solutions

Instructor: Dmitri Svergun , European Molecular Biology Laboratory, Hamburg

Slides:

• Slides: Basic
• Slides: Abinitio
• Slides: Rigid

Topics: Small-angle X-ray scattering (SAXS): basics. Calculation of overall paramaters and ab initio low resolution shapes. Rigid body modelling and quaternary structure analysis of complexes. Quantitative characterization of mixtures and flexible systems. Hybrid use of SAXS with other structural and biochemical techniques.

 

[Wednesday the 10th] Computational Modeling of large Multimolecular Assemblies based on Multi-resolution Experimental Data

Instructor: Haim Wolfson , Tel Aviv University

Slides:

• Part I
• Part II
• Part III

Topics: Protein-protein docking. Integrative modeling of large multimolecular assemblies.

 

[Thursday the 11th] Integrative Approaches to Macromolecular Modeling

Instructor: Riccardo Pellarin, Institut Pasteur Paris

Slides:

• Slides

Topics: The four stage approach: gathering data, representing the system and translating data into a scoring function, sampling configurations and analysis of models. Bayesian scoring functions: modeling structural heterogeneity, data noise, data ambiguity, and sparseness. Structure determination of protein assemblies using chemical cross-linking and electron microscopy data Examples using the Integrative Modeling Platform.

 

[Friday the 12th] Modeling Contacts in Macro-molecular assemblies: from Inference to Assessment

Instructor: Frédéric Cazals , Algorithms-Biology-Structure, Inria Sophia Antipolis

Slides:

• Slides

Topics: Connectivity inference from native mass spectrometry and tandem affinity purification data. Handling uncertainties in reconstructions of macro-molecular assembly models. Probing macro-moleclular assembly models with graph templates of sub-complexes. Comparing scoring landscapes.