Pierre POULAIN
Professional address
DSIMB team
Inserm UMR-S 665 and Université Paris Diderot - Paris 7
INTS
6, rue Alexandre Cabanel
75015 Paris
France
e-mail: pierre DOT poulain AT univ-paris-diderot DOT fr
Link to research/teaching webpage @ DSIMB
Research activities
2007 - to present
Lecturer at the University Paris Diderot - Paris 7
Research performed in the DSIMB team part of the Inserm U665 lab (Inserm and University Paris Diderot - Paris 7), Paris, France.
topics: macromolecular assemblies
collaborators: D. Flatters, JC Gelly, C. Etchebest, L. Montout
2006 - 2007
Post-doc at Laboratoire de Biochimie Théorique , UPR 9080 CNRS, Paris, France.
topics : flexible protein/DNA docking
collaborators : A. Saladin and C. Prévost
- A. Saladin, S. Fiorucci, P. Poulain, C. Prévost, and M. Zacharias,
PTools: an opensource molecular docking library,
BMC Structural Biology 9: 27 (2009).
[DOI: 10.1186/1472-6807-9-27] [PMID: 19409097] - P. Poulain, A. Saladin, B. Hartmann, and C. Prévost,
Insights on protein-DNA recognition by coarse grain modelling
Journal of Computational Chemistry 29: 2582-2592 (2008).
[PDF, 594 Kb] [DOI: 10.1002/jcc.21014] [PMID: 18478582]
2003 - 2006
PhD student at Laboratoire de spectrométie ionique et moléculaire (Lasim) , UMR 5579, CNRS and Université Lyon 1, France.
topics : statistical approach of the structure and dynamics of isolated proteines
supervisor: P. Dugourd ("Electric dipole, biomolecules and clusters" group)
abstract : this work is a theoretical study of the thermodynamical properties of polypeptides in the gas phase. We aim to a better understanding of the fundamental mechanisms involved in protein folding. A statistical approach base on Monte Carlo algorithms applied in generalised ensembles, such as Replica Exchange Method or Wang-Landau method, has been used to sample the rugged energy landscape of those molecules. The peptides were composed of 2 to 20 amino acids and have been modelised by the Amber 96 forcefield. Simulations have been realised in strong relation with experimental progress of the group. We thus tried to understand the influence of the secondary structure on photofragmentation mechanism, the role of entropy in the stabilisation of beta sheets ans the effect of intense and static electric field on peptide conformation.
Download my PhD thesis locally [PDF, 4.9 Mb, french] or on the CNRS TEL multidisciplinary thesis server
- F. Calvo, and P. Poulain,
Transitions between secondary structures in isolated polyalanines
The European Physical Journal D 51: 15-23 (2009).
[PDF, 454 Kb] [DOI: 10.1140/epjd/e2008-00096-0] - P. Poulain, F. Calvo, R. Antoine, M. Broyer, and P. Dugourd,
Competition between secondary structures in gas phase polyalanines
Europhysics Letters 79:66003 (2007).
[PDF, 350 Kb] [DOI: 10.1209/0295-5075/79/66003] - P. Poulain, F. Calvo, P. Dugourd, R. Antoine, and M. Broyer,
Performances of Wang-Landau algorithms for continuous systems,
Physical Review E 73: 056704 (2006).
[PDF, 614 Kb] [DOI: 10.1103/PhysRevE.73.056704] [PMID: 16803071] - R. Antoine, M. Broyer, J. Chamot-Rooke, C. Dedonder, C. Desfrancois, P. Dugourd, G. Gregoire, C. Jouvet, P. Poulain, T. Tabarin, and G. Van der Rest,
Comparison of the fragmentation pattern induced by collisions, laser excitation and electron capture. Influence of the initial excitation,
Rapid Communications in Mass Spectrometry 20: 1-5 (2006).
[PDF, 167 Kb] [DOI: 10.1002/rcm.2489] [PMID: 16637002] - P. Poulain, R. Antoine, M. Broyer, and P. Dugourd,
Monte Carlo simulations of flexible molecules in a static electric field: electric dipole and conformation,
Chemical Physics Letters 400: 1-6 (2005).
[PDF, 333 Kb] [DOI: 10.1016/j.cplett.2004.11.025]
March - September 2003
Biomolecular Sciences department, UMIST, Manchester, UK
topics: automatic extraction of the toxic properties of compounds from the biomedical literature
supervisor: B. J. Stapley
abstract: Automatic information extraction from free-text documents encompasse a set of techniques and tools already well known, but its application to biology is relatively new. Thus, this project aims to predict and/or extract toxicological properties of some compounds using information extraction and retrieval techniques. Nowadays, toxicological data are issued from in vitro and in vivo tests that are expensive and time-consuming for the pharmaceutical industry. As a consequence, and given the large body of information latent in bibliographic databases, the prediction of toxic information on possible therapeutic compounds becomes particularly important.
July - August 2001
Laboratoire d'ImmunoGénétique Moléculaire (LIGM) , Montpellier, France.
topics: 3D visualization tools for IMGT structural data
supervisors: M. Ruiz and M.-P. Lefranc
abstract: IMGT (http://imgt.cines.fr), the international ImMunoGeneTics database is an integrated database, specializing in immunoglobulins (Ig), T-cells receptors (TcR) and major histocompatibily complex (MHC) molecules of all species that was created in 1989 by Marie-Paule Lefranc (Montpellier II Unversity, CNRS, Montpellier, France)
We aim to implement PERL scripts in order to compare 3D structures of proteins picked up in the IMGT database (use of STAMP).
Teaching activities
2007 - to present
Université Paris Diderot - Paris 7.
2003 - 2006
Multidisciplanary engineering university Institut National des Sciences Appliquées de Lyon (INSA Lyon)
First year chemistry workshops (288 hours, 255 students).
22 - 27/05/2005
Summer school Modelisation, dynamique et thermodynamique des agrégats et molécules complexes
Modelisation workshop: simulated annealing and parallel tempering simulations of a dipeptide.
Academic training
2003 - 2006
PhD in Physics, Lasim, Université Lyon 1, France
2002 - 2003
MSc in Cheminformatics, UMIST, Manchester, U.K.
2000 - 2003
"Diplôme d'Ingénieur Chimiste" at the
Ecole Nationale Supérieure de Chimie de Montpellier (the National Graduate School of Chemistry, Montpellier)
http://www.enscm.fr/international_website.htm
1997 - 2000
Classes Préparatoires aux Grandes Ecoles, preparatory classes leading to French institutes.
Lycée Henri Bergson, Angers, France.
1997
Baccalauréat in Sciences, i.e. High School diploma
Lycée David d'Angers, France.
Languages
- French: native fluency
- English: good level in spoken and written English
Computers skills
- operating systems [administration]: GNU/Linux (Fedora Core, Debian, Ubuntu, Mandriva)
- office software: Microsoft Office and OpenOffice.org
- programming: C++, Python
- molecular visualisation: Rasmol, Pymol
- misc.: gnuplot, xmgrace, R, LaTeX