O'DONNELL , Timothée

This thesis introduces the first global parametric model of protein loops amenable to effective sampling strategies a-la Hit-and-Run, making four contributions. Starting with the classical kinematic view of loop closure developed by Coutsias et al, the first one resides in a geometric analysis of the Tripeptide Loop Closure (TLC) problem in...

Abstract Flexible loops are paramount to protein functions, with action modes ranging from localized dynamics contributing to the free energy of the system, to large amplitude conformational changes accounting for the repositioning whole secondary structure elements or protein domains. However, generating diverse and low energy loops remains a...

The center of mass of a point set lying on a manifold generalizes the celebrated Euclidean centroid, and is ubiquitous in statistical analysis in non Euclidean spaces. In this note, we give a complete characterization of the weighted p-mean of a finite set of angular values on S 1 , based on a decomposition of S 1 such that the functional of...

Abstract Designing movesets providing high quality protein conformations remains a hard problem, especially when it comes to deform a long protein backbone segment, and a key building block to do so is the so‐called tripeptide loop closure (TLC). Consider a tripeptide whose first and last bonds ( and ) are fixed, and so are all internal...