Lectures

To kick things off, each participant is expected to provide a 5-minute presentation of their research interests on Sunday evening.

The morning sessions (Monday to Friday, starting at 9h) will be devoted to the following lectures:

Monday: T. Simonson, Introduction to computational protein design and accurate energy models

Tuesday: T. Schiex, Advanced combinatorial optimization methods for protein design

Wednesday: T. Kortemme, Flexible backbone protein design

Thursday: Y. Zhang, Evolutionary design of functional proteins

Friday: Cortés-Robert-Cazals, Exploration and characterization of energy landscapes to assess protein design strategies

 


 

Monday: Introduction to computational protein design and accurate energy models

Lecture-Simonson

Instructors:

Topics:

  • CPD:goals and ingredients
  • Basic methods:
    • folded and unfolded proteins
    • energy and solvent model
    • deterministic and stochastic search strategies
    • software packages: Rosetta and the rest
  • More advanced methods:
    • acid/base, redox, and ligand mutations
    • many body effects: Generalized Born solvent, polarizable molecular mechanics
    • importance sampling and free energies
  • Illustrative applications
    • whole protein design and benchmarking
    • aminoacyl-tRNA synthetase, PDZ design

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Tuesday: Advanced combinatorial optimization methods for protein design

Lecture-Schiex

Instructor:

Topics:

  • Presentations of recent optimization and counting methods from Artificial Intelligence that can find guaranteed Global Minimum Energy Sequence-Conformations on redesign problems of medium size on a single CPU core
  • Variants of these methods able to offer epsilon-guaranteed or probably approximately correct (delta,epsilon) guaranteed approximations of the partition function, a proxy to free energy and binding affinity estimation

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 Wednesday: Flexible backbone protein design

Lecture_Kortemme

Instructor:

Topics:

  • Design of new structures and functions: state-of-the-art and challenges
  • Methods to model small conformational adjustments critical for design
  • Methods to predict and design larger conformational changes
  • Reshaping existing proteins and creating new functions
  • Designing sequences consistent with multiple conformations

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Thursday: Evolutionary design of functional proteins

 Lecture-Zhang

Instructor:

Topics:

  • Characterizing protein evolution using structural profiles
  • Evolutionary design of protein folds
  • Introducing functions to protein fold design
  • Redesigning caspase-9 associated apoptosis pathways

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 Friday: Exploration and characterization of energy landscapes to assess protein design strategies

Lecture-Cortes-Cazals 

Instructors:

 Topics:

  • Exploring the conformational space of proteins: a quick overview of available methods
  • Sampling energy landscapes with robotics-inspired algorithms
  • Persistence based analysis of energy/scoring landscapes
  • Comparison of energy/scoring landscapes
  • Comparison of clusterings

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