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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
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
Tuesday: Advanced combinatorial optimization methods for protein design
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
Wednesday: Flexible backbone protein design
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
Thursday: Evolutionary design of functional proteins
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
Friday: Exploration and characterization of energy landscapes to assess protein design strategies
Instructors:
- Juan Cortés, Robotics and Interactions Group, LAAS-CNRS, Toulouse (France)
- Charles H. Robert, Laboratory of Theoretical Biochemistry, CNRS, Paris (France)
- Frédéric Cazals, Algorithms-Biology-Structure, INRIA, Sophia-Antipolis (France)
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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