CECAM workshop on Flexible Macromolecular Docking
April 28-30, 2004
Lyon, France


 

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Workshop program



Session 1:  Presentation and analysis of the possible types of deformations which can be expected to occur within macromolecules during their association. Analysis of the impact of such deformations on the results of the CAPRI Contest; examples where conformational changes have or have not impeded good prediction.

Session 2:  How flexibility is accounted for in the present docking methods :
       -  implicitly or explicitly
       -  at the level of side-chains, loops or domain
       -  at the refinement stage or during the docking process

Session 3: Possible methods that can be used to treat protein flexibility at different levels : local or global, full-atom or reduced representation, harmonic or anharmonic movements; experience accumulated in neighboring fields, small ligand docking or protein folding.
 

Wednesday 28th April 
 

8.45 - 9.00 Welcome and practical information  
9.00 - 9.20 Chantal Prévost
Presentation of the workshop: principal issues and objectives
 
9.20 - 9.55 Joël Janin
Conformation changes and specificity of protein-protein interaction
Abstract
9.55- 10.30 Shoshana Wodak
Possible types of protein deformations and summary of some of the 
CAPRI results with focus on the influence of conformational changes.
Abstract
10.30 - 11.00 Coffee break  
11.00 - 11.35 Miriam Eisenstein
Analysis of the impact of deformations on the results of the CAPRI contest 
Abstract
11.35 - 12.10  Carlos J. Camacho
How Flexible your Rigid-Body Docking Should Be
Abstract
12.10 - 14.15 Lunch break  
14.15 - 14.50 Juan Fernández-Recio
ICM optimization of flexible interface side-chains in protein-protein docking: 
successes and limitations
Abstract
14.50 - 15.25 Ludwig Kripphal
Flexibility as part of the geometric filtering problem
Abstract
15.25 - 17.00 Poster session and coffee break
Posters
17.00 - 17.35 Michael J.E. Sternberg
Modelling the structure of protein-protein complexes
Abstract

Thursday 29th April 
 

9.00 - 9.35 Ruben Abagyan
Simulating induced fit in molecular docking
 Abstract
9.35 - 10.10 Dina Schneidman
Modeling large-scale hinge-bent motions in docking
 Abstract
10.10 - 10.30 Discussion session
 
10.30 - 10.50 Coffee break  
10.50 - 11.25 Karine Bastard
Accounting for protein loop flexibility during macromolecular docking
 Abstract
11.25 - 12.00 Martin Zacharias
How to efficiently account for side chain flexibility and global motions
during docking
 Abstract
12.00 - 14.00 Lunch break and poster session
 Posters
14.00 - 14.35 Alexandre M.J.J Bonvin
HADDOCK: an information-driven flexible docking approach
 Abstract
14.35 - 15.10 Graham R. Smith
How may the use of MD and rigid-body docking algorithms overcome 
the protein flexibility problem associated with complex formation? 
 Abstract
15.10 -19.30 Afternoon free  
19.30 Dinner  

Friday 30th April 
 

9.00 - 9.35 Yuval Inbar
Combinatorial docking for multi-molecular assembly and protein structure prediction
Abstract
9.35 - 10.10 Raik Gruenberg
Complementarity of structure ensembles in protein-protein binding
Abstract
10.10 - 10.30 Discussion session  
10.30 - 10.50 Coffee break  
10.50 - 11.25 Olivier Lichtarge
Prediction of interacting surfaces by the Evolutionary Trace method
Abstract
11.25 - 12.00 Leslie Kuhn
Modeling Correlated Protein Main-chain Motions in Proteins and their Ligands 
Abstract
12.00 - 13.30 Lunch break  
13.30 - 14.05 Heather A. Carlson
Protein flexibility and drug design: How to hit a moving target
Abstract
14.05 - 15.05 Discussion session  
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