1. Computational Protein Design
4. Practical Exercise
Pablo Carbonell
pablo.carbonell@issb.genopole.fr
iSSB, Institute of Systems and Synthetic Biology
Genopole, University d’Évry-Val d’Essonne, France
mSSB: December 2010
Pablo Carbonell (iSSB) Computational Protein Design mSSB: December 2010 1/4

2. Objective: A Primer to the In Silico Protein Design Cycle
1 Problem formulation. Analysis of binding regions of a protein of interest.
2 Model building. Prediction of hot-spots of affinity from the structal model of
the interacting complex between the protein and its partner.
3 Design. Perform an in silico saturation mutagenesis for key residues and
select best variants.
4 Validation. Database and literature search, in order to compare predictions
with experimental mutagenesis data.
5 Implementation. Implement a protein design strategy.
Pablo Carbonell (iSSB) Computational Protein Design mSSB: December 2010 2/4

3. Let’s do it!
Please, proceed to:
http://bioretrosynth.issb.genopole.fr/wiki/MSSBProtDes2010
... and good luck!!!
Pablo Carbonell (iSSB) Computational Protein Design mSSB: December 2010 3/4

4. Computational Protein Design
4. Practical Exercise
Pablo Carbonell
pablo.carbonell@issb.genopole.fr
iSSB, Institute of Systems and Synthetic Biology
Genopole, University d’Évry-Val d’Essonne, France
mSSB: December 2010
Pablo Carbonell (iSSB) Computational Protein Design mSSB: December 2010 4/4