Dr. Anne Poupon
Yeast Structural Genomics Laboratory
IBBMC, Bât 430,
Université Paris-Sud
91405 0rsay
France
tel: 33 1 69 15 31 56
fax: 33 1 69 85 37 15
email: anne.poupon@u-psud.fr
http://genomics.eu.org/spip/Anne-Poupon
Development of protein-protein docking algorithms
The functions of most protein are subordinated to the interaction with one or more partners: small molecules, other proteins, nucleic acids, etc. Protein-protein complexes are involved in many cellular processes and consequently are of great interest for the biochemical and biological functionnal study of their components. As of today, while structural genomics projects increases dramatically the number of isolated protein structures, still very little is known on the multimolecular assemblies. More... .
Compute the score of a given complex conformation here
Development of new algorithms for the detection of unfolded regions in protein sequences 
One condition required for the experimental resolution of a protein’s three dimensional structure is its ability to fold in a stable conformation. Many proteins consist in multiple structural domains separated by flexible regions. In this case, the experimental structural study of the complete protein is not possible. The individual domains have to be studied separately. However, there’s no available method to accurately detect the limits of these domains. Indeed, must of the available methods are based on sequence comparison. more
Use Prelink to predict unfolded regions in a sequence here
HalX: a LIMS for structural biology 
Data management has been identified as a crucial issue in all large scale experimental projects. In this type of project, many different persons manipulate multiple objects in different locations; thus, unless complete and accurate records are maintained, it is extremely difficult to understand exactly what has been done, when it was done, who did it, and what exact protocol was used. All of this information is essential for use in publications, for reusing successful protocols, for determining why a target has failed, and for validating and optimizing protocols. Although data management solutions have been in place for certain focused activities, for example genome sequencing and microarray experiments, they are just emerging for more widespread projects, such as structural genomics, metabolomics, and systems biology as a whole. The complexity of experimental procedures, and the diversity and high rate of development of protocols used in a single centre, or across various centres, have important consequences for the design of information management systems. Because procedures are carried out both by machines and by hand, the system must be capable of handling data entry both from robotic systems and by means of a user-friendly interface. The information management system needs to be flexible so that it can handle changes in existing protocols or newly added protocols. Because no commercial information management systems have had the needed features, most structural genomics groups have developed their own solutions. More
Download, install and documentation here
Rafale: methods for semi-automated function assignment 
Genome annotation consists in the characterization of the functions of genes and gene products and the biological proceses they participate in. This requires taking into account all the available information. Annotation thus requires integration of various, massive and herterogeneous data from four main sources:
The objective of the Rafale project is to assist biologists in the complex task of integration by improving the interaction between the system and the human expert. As of today, the annotation process relies entirely on the expert who validates, confronts and integrates data and results produced by the system to give a coherent annotation. more
Graduated from Ecole Normale Supérieure (Biology)
University degree in Cellular and Molecular Biology
University degree in Mathematics and Informatics
Master’s degree in Biomathematics
Ph.D. in Biomathematics
1991 : Training period (3 months) in molecular biology, under the direction of Dr. Victor Ling
Princess Margareth Hospital, Toronto, Canada
1994-1998 : Ph.D. in Biomathematics, under the direction of Dr. Jean-Paul Mornon,
Equipe Systèmes Moléculaires et Biologie Structurale
Laboratoire de Minéralogie-Cristallographie, UMR C7590, Universités Paris 6 et 7,
Dissertation topic: Hydrophobic invariants in globular proteins core
1998-1999 : Post-doctoral fellow, under the direction of Dr. Bernard Gilquin, Laboratoire de Structure des Protéines, Département d’Ingénierie et d’Etude des Protéines (DIEP), CEA/SACLAY
Research topic: Automatic determination of mutation sites for the creation of new enzymatic activities.
Since october 2000 : Reseacher CNRS - section 07 (Informatics)
Equipe Génomique Structurale (group leader: Herman van Tilbeurgh) - Institut de Biophysique et de Biologie Moléculaire et Cellulaire (head: Lucienne Letellier).
January - july 2005: training period in Dr. Alwyn Jones laboratory, Univeristy of Uppsala, Sweden. Design of a data model for crystallization and crystallography.