WINTER SCHOOL ALGORITHMS
IN STRUCTURAL BIOINFORMATICS :

MODELING ANTIBODIES AND THEIR COMPLEXES

14-18 november 2016, Inria Sophia Antipolis, France

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[Daily Schedule]

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

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[Monday the 14th] Standards and tools for sequences and 3D structures of immunoglobulins: IMGT®, the international ImMunoGeneTics information system

Instructors: Marie-Paule Lefranc and Patrice Duroux, CNRS and University of Montpellier -- IMGT

Slides:

Topics: Immunoglobulins: a primer, IMGT, the international ImMunoGeneTics information system, Analyzing sequences of IG, Analyzing structures of IG.

 

[Tuesday the 15th] Basic concepts and novel algorithms for modeling antibodies and their interactions

Instructors: Charles H. Robert, CNRS / IBPC, France Juan Cortés, LAAS / CNRS, Toulouse, France

Slides:

Topics: Biophysics of protein interactions: a primer, Docking algorithms, Modeling proteins as robots to enhance conformational sampling, Cost-based motion-planning algorithms to efficiently compute transition paths of highly flexible molecules.

 

[Wednesday the 16th] Modeling antibody - antigen complexes: predicting binding affinity and interaction specificity

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

Slides:

Topics: Modeling interfaces of macro-molecular complexes, Basics in regression analysis, Basics in geometric modeling with Voronoi diagrams, Predicting binding affinities for IG - Ag complexes, Analyzing the interaction specificity of IG, Corresponding tools in the Structural Bioinformatics Library.

 

[Thursday the 17th] In-silico structure based design of antibodies

Instructor: Charlotte Deane, Oxford University

Slides:

Topics: SABDAB – the antibody structure database, ABodybuilder -- automated antibody structure prediction with data-driven accuracy estimation, Orientating the VH and VL domains, Predicting CDR-H3 rapidly and accurately, Paratopes and Epitopes – predicting and designing binding.

 

[Friday the 18th] Visualizing binding assay data using antigenic cartography

Instructor: David F. Burke, Cambridge University

Slides:

Topics: Theory of antigenic cartography, Influenza viruses, Example application: understanding the antigenic drift of influenza viruses.