Link to research/teaching webpage @ DSIMB

supervisors: M. Ruiz and M.-P. Lefranc \\

• 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]

http://pierrepoulain.free.fr/cv/poulain.jpg

http://pierrepoulain.free.fr/cv/poulain.jpg |

http://pierrepoulain.free.fr/cv/poulain.jpg | Rock on!

http://pierrepoulain.free.fr/cv/poulain.jpg | Rock on!

http://www.enscm.fr/international_website.htm

DSIMB team \\

INTS \\

Université Paris Diderot - Paris 7.

First year chemistry workshops (288 hours, 255 students).

"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 | http://www.enscm.fr/international_website.htm]]

Pierre POULAIN

 P. Dugourd, G. Gregoire, C. Jouvet, P. Poulain, T. Tabarin, and G. Van der Rest, \\

July - August 2001 \\

 [DOI: 10.1209/0295-5075/79/66003]

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.

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. \\

• 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)

Teaching activities

2007 - to present \\

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 \\

Academic training

2003 - 2006 \\

2002 - 2003\\

2000 - 2003
"Diplôme d'Ingénieur Chimiste" at the Ecole Nationale Supérieure de Chimie de Montpellier (the National Graduate School of Chemistry, Montpellier) \\

1997 - 2000 \\

1997
Baccalauréat in Sciences, i.e. High School diploma \\

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

Personal interests

• Cooking: spice bread, blueberry muffins, bananas flambe pie, pear-chocolat cake, indian curry, vegetables and chicken crumble, home made pizza, ...
• Fitness (step, LIA, streching), running and swimming

 [DOI: 10.1140/epjd/e2008-00096-0]

multidisciplinary thesis server

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

• 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 \

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] \\

• March - September 2003

 [PDF, 4.9 Mb, french]  or on the CNRS TEL   multidisciplinary thesis server \\

  [DOI: 10.1209/0295-5075/79/66003] \\

  * F. Calvo, and P. Poulain, \\

  * P. Poulain, F. Calvo, R. Antoine, M. Broyer, and P. Dugourd, \\

 * 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] 

or on the CNRS TEL multidisciplinary thesis server \\

 topics: macromolecular assemblies 
 collaborators: D. Flatters, JC Gelly, C. Etchebest, L. Montout

 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,

 :topics: macromolecular assemblies 
 :collaborators: D. Flatters, JC Gelly, C. Etchebest, L. Montout

 supervisor: P. Dugourd \

  [PMID: 18478582]

  [PDF, 594 Kb]   [DOI: 10.1002/jcc.21014]   PMID: 18478582

  [PDF, 594 Kb]   DOI: 10.1002/jcc.21014 \

  * P. Poulain, A. Saladin, B. Hartmann, and C. Prévost, \\

 ** P. Poulain, A. Saladin, B. Hartmann, and C. Prévost, \\

 collaborators : A. Saladin and C. Prévost

 * 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. \\

• 2007 - to present \\

 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
  ''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 ''

• 2007 - to present\\

• 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, C. Etchebest, L. Montout

2007 - to present

lecturer at the University Paris Diderot - Paris 7

Professional address

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, C. Etchebest, L. Montout

2006 - 2007,

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

Research activities

2007 - to present Lecturer at the University Paris Diderot - Paris 7

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

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. Macromolecular assemblies (with D. Flatters, C. Etchebest, L. Montout, B. Hartmann and M. Guéroult) 2006 - 2007

Post-doc at Laboratoire de Biochimie Théorique , UPR 9080 CNRS, Paris, France Flexible protein/DNA docking (with A. Saladin and C. Prévost)

paper5

    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 Statistical approach of the structure and dynamics of isolated proteines (supervisor P. Dugourd). P. Dugourd's group: "Electric dipole, biomolecules and clusters" group 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

paper6

    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] 

paper4

    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] 

paper3

    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] 

paper2

    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] 

paper1

    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 Automatic extraction of the toxic properties of compounds from the biomedical literature (supervisor B. J. Stapley) 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 3D visualization tools for IMGT structural data (supervisors M. Ruiz and M.-P. Lefranc) 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

Personal interests

    * Cooking: spice bread, blueberry muffins, bananas flambe pie, pear-chocolat cake, indian curry, vegetables and chicken crumble, home made pizza, ...
    * Fitness (step, LIA, streching), running and swimming