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Scientific Fields
Diseases
Organisms
Applications
Technique
Date
27
Apr 2017
Time
14:00:00
25 Rue du Dr Roux, Paris, France
Address
Building: Amphithéâtre Jacques Monod, sous-sol bâtiment MONOD 66
Location
2017-04-27 14:00:00 2017-04-27 16:00:00 Europe/Paris Computational geometry for the determination of biomolecular structures     Structural biology is centrally concerned with the description of a biomolecule’s geometry, as angles and distances between the biomolecule’s atoms are measured in order to determine the biomolecular structure. The values of […] 25 Rue du Dr Roux, Paris, France Benjamin Bardiaux benjamin.bardiaux@pasteur.fr

About

 
 
Structural biology is centrally concerned with the description of a biomolecule’s geometry, as angles and distances between the biomolecule’s atoms are measured in order to determine the biomolecular structure. The values of these geometrical parameters may be obtained from biophysical techniques, such as Nuclear Magnetic Resonance spectroscopy. In this PhD project, the performances of a new computational method for protein structure calculation was delved. This method, implemented within the iBPprot software framework, treats protein structure determination as a distance geometry problem, which
the interval branch-&-prune algorithm tries to solve by the full exploration of its solutions space. The results obtained by iBPprot on a set of proteins, with sizes up to 120 residues and displaying various secondary structures and topologies, was analyzed. Using short-range exact distance restraints, it was possible to rebuild the structure of all protein targets, and for many of them it was possible to exhaustively explore their conformational spaces. Because exact distance restraints are not always possible to procure from experimental techniques, the method was then tested with interval data restraints. In this case,iBPprot permitted an exploration of more than 70% of the conformational space size for most of the targets. Furthermore, conformations closer than 5Å to the target conformations were obtained. The quality of the generated structures was satisfactory with respect to Ramachandran plots, but arguable because of the presence of steric clashes in some conformers. The runtime over most performed calculations was competitive with existing structure determination method.
 

 

Location

Building: Amphithéâtre Jacques Monod, sous-sol bâtiment MONOD 66
Address: 25 Rue du Dr Roux, Paris, France