Extending Distance Geometry methods: not only distances (A study of three applications with a focus on structural biology)

Type de soutenance
Thèse
Date de début
Date de fin
Lieu
IRISA Rennes
Salle
Markov
Orateur
Simon Hengeveld
Département principal
Sujet

We study different aspects of the Distance Geometry Problem (DGP). The DGP is an inverse problem where a set of pairwise distances is inverted to find a structure in a Euclidean space, given a certain dimension K. Our main focus lies on the application of structural biology, where we can exploit inter-atomic distances to compute protein structures. For this application, we are able to discretize the search space using branch-and-prune methods. We extend the method to not only use distance information but also torsion angles. We present experiments using real NMR data with promising results. Next, we look at dynamical Distance Geometry with a main focus on human motions, laying the groundwork for future projects which could focus on modeling protein dynamics. Furthermore, we discuss adaptive maps, which is another example of an application of DG in which we can exploit more than just distance information.

Composition du jury
Rapporteurs avant soutenance :
Adrien GOËFFON - Professeur des universités (HDR), LERIA/Université d’Angers
Juan CORTÉS - Directeur de Recherches (HDR), LAAS-CNRS à Toulouse

Examinateurs :
Adrien GOËFFON - Professeur des universités (HDR), LERIA/Université d’Angers
Juan CORTÉS - Directeur de Recherches (HDR), LAAS-CNRS à Toulouse
Douglas GONÇALVES - Professeur, Universidade Federal de Santa Catarina
Silvia BOTTINI - Chaire de professeur junior (CPJ), INRAE à Nice
Thérèse MALLIAVIN -Directeur de Recherches (HDR), LORIA-CNRS à Nancy

Dir. de thèse :
Antonio MUCHERINO - Maître de conférence (HDR), IRISA/Université de Rennes