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Algorithms in Structural Bio-informatics :

Winter School

2-7 december 2012, Inria Sophia Antipolis, France

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The first afternoon (Dec. the 2nd) will be devoted to short presentations. Each of the five remaining days will be organized as follows:

  • Lecture from 9am to 10:30am, and from 10:45 am to noon
  • Lunch at 12:45pm (sharp!)
  • Practical from 2pm to 5:30pm

[Sunday the 2nd, 2pm - 6:30pm] Short presentations by the participants (7'+3')

[Monday the 3rd] I. Obtaining and organizing structural information for modeling studies


  • The Protein Data Bank and related resources
  • Organizing and manipulating protein structural data and derived quantities
  • Data structures for higher-level problems
Projects proposed:
  • Analyzing conformational changes in protein-protein association
  • Correlating observed structural changes and collective movements of proteins


[Tuesday the 4th] II. Modeling protein complexes and assembies with Voronoï diagrams


  • Affine and curved Voronoi diagrams: a primer.
  • Modeling atomic resolution protein interfaces and binding patches.
  • Modeling fuzzy protein assemblies in the context of reconstruction by data integration.
Projects proposed:
  • Investigating complexes from the immune system, annotated in the IMGT/3Dstructure-DataBase
  • Spotting putative binding patches on orphan proteins.


[Wednesday the 5th] III. Molecules as robots: mining the flexibility of proteins


  • Some basic notions on robot modeling and motion planning algorithms.
  • Robotics-inspired methods to explore the conformational space of proteins.
  • Investigating the accessibility to active sites considering flexible molecule models.
Projects proposed:
  • Computing conformational transitions of proteins.
  • Simulating ligand (un)binding with a single processor.


[Thursday the 6th] IV. Structural comparisons


  • Integer programming modeling and relaxations
  • Application to the study of protein structures
  • Application to the study of protein binding patches
Projects proposed:


[Friday the 7th] V. Docking algorithms


  • Macromolecular docking methods: principles and state of the art
  • Coarse-grained representations of proteins and nucleic acids
  • The ATTRACT/PTools docking suite
Project proposed:
  • Systematic docking including side chain and global flexibility
  • Docking multiple partners
  • Construction of protein filaments: from two-component docking to the generation of full helices