Using the Voronoi tesselation for the modeling of protein-protein complexes
type: Dataset
description: The function of a protein is often subordinated to its interaction with one or many partners. Yet, the tridimensional structure study of this complexes, that can't be done experimentally, would permit the understanding of many cellular processes. This work contains two parts. The first part concerns the setting up of a scoring function for protein-protein docking and the second part concerns the crystallographic structure study of a tetrameric protein : the Paramecium Bursaria Chlorella Virus thymidylate synthase X, a potential antibacterial target. Docking of protein-protein complexes consists in two successive steps : first a large number of putative conformations are generated, then a scoring function is applied to rank them. This scoring function has to take into account both geometric complementarity of the two molecules and physico-chemical properties of surfaces in interaction. We addressed the second step of this problem through the development of a quick and reliable scoring function. This was done using Voronoi tessellation of the tridimensional structure of the proteins. Voronoi or Laguerre tessellations were shown to be good mathematical models of protein structure. In particular, this formalization leads to a good description of structural properties of the residues. This modeling illustrates the packing of the residues at the interface between two proteins. Thus, it is possible to measure a set of parameters, on protein-protein complexes whose structure is known, and on decoys. These parameters are frequencies of residues and pair frequencies of the residues at the interface, volumes of Voronoi cells, distances between residues at the interface, interface area and number of residues at the interface. They were used as input in statistical machine learning procedures (logistic learning, support vector machines (SVM) and genetic algorithms). These led to efficient scoring functions, able to separate native structures from decoys. In the second part, I de…
landing page: https://theses.hal.science/tel-00804990
identifier: NNT: 2006PA112029
keyword: complexes-proteines-proteines
keyword: infoeu-reposemanticsdoctoralthesis
keyword: infoinfo-bicomputer-science-csbioinformatics-q-bioqm
keyword: interactions
keyword: machine-learning-procedures
keyword: procedures-dapprentissage
keyword: protein-protein-complexes
keyword: sdvbbmbclife-sciences-q-biobiochemistry-molecular-biologybiochemistry-q-biobm
keyword: sdvbbmbplife-sciences-q-biobiochemistry-molecular-biologybiophysics
keyword: sdvbibslife-sciences-q-bioquantitative-methods-q-bioqm
keyword: tessellation-de-voronoi
keyword: theses
keyword: thymidylate-synthase-x
keyword: voronoi-tessellation
issued: 2026-05-12T02:44:46.559944
modified: 2026-05-12T02:44:46.559950
language: fr
contact point: Organization
  fn: CCSD

test_moissonnage_selune
type: Agent

Using the Voronoi tesselation for the modeling of protein-protein complexes
type: Distribution
format: HTML
access URL: https://theses.hal.science/tel-00804990
issued: 2026-05-12T02:44:46.649225
modified: 2026-05-12T02:44:46.520355