logo Inria

Algorithms in Structural Bio-informatics :

Winter School

2-7 december 2012, Inria Sophia Antipolis, France

 logo CNRS
 
 
 
 

    Agenda

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

Instructors:

Topics:
  • 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

Instructor:

Topics:
  • 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

Instructor:

Topics:
  • 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

Instructors:

Topics:
  • 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

Instructors:

Topics:
  • 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

 
webmaster