Intern - Chemosim Lab

Aroma Perfume Synthesis and Modelling (APSM) Group
Institut de Chimie de Nice (ICN), Mixed research unit (UMR) 7272
Université Côte d'Azur (UCA), Nice, France

Description

Molecular and numerical models of chemosensory perceptions

Skills

  • Web-development:
    • Creating a responsive webpage with Bootstrap
    • Developing a web server with Django framework, and deploying it with Gunicorn and Nginx
    • Integrating a website with a relational PostgreSQL database
    • Implementing a distributed job queue with Celery
  • Machine-learning:
    • Designing QSAR/QSPR classification and regression models:
      • Development: data curation, feature normalisation/scaling, feature selection, machine-learning methods
      • Validation: chance correlation, preparation of training and test sets, N-fold cross-validation
      • Application: applicability domain
    • Benchmarking and optimizing different classifiers
    • Visualizing high-dimensional data with PCA and SOM
  • Chemoinformatics:
    • Calculating structural and physicochemical descriptors
    • Extracting a diverse subset of molecules from a large dataset
  • Bioinformatics: constructing multiple sequence alignment of proteins
  • Molecular Modelling:
    • Creating homology models of proteins from sequence alignments
    • Embedding a protein in a membrane
    • Running molecular dynamics (MD) simulations with AmberTools and Amber:
      • Constructing topology and coordinates files with tLEaP
      • Submitting simulations with pmemd on multiple CPUs or GPUs
      • Analyzing simulations with cpptraj
  • System Administration: installing a Linux operating system, drivers, and compiling programs on a computer

Tools

Coworkers

Internship supervisor: Sébastien Fiorucci
Members: Serge Antonczak, Jérôme Golebiowski, Jérémie Topin, Xiaojing Cong, Caroline Bushdid
Interns: Ourvashi Kissoondoyal, Armelle Cugnod, Laura Darner, Bertille Fourel, Xiaojun Mao

February 2018 - July 2018

Technician - IFM Lab

Laboratoire d'Ingénierie des fonctions moléculaires (IFM Lab)
Institut de Sciences et d'Ingénierie Supramoléculaires (ISIS), UMR 7006
Université de Strasbourg, France

Description

Development of computational chemistry workflows

Skills

See ChemFlow for more details

Coworkers

Supervisor: Marco Cecchini
Members: Diego Enry Barreto Gomes, Nicolas Martin, Adrien Cerdan, Florian Blanc, Joel Montalvo Acosta
Interns: Paulina Pacak

July 2017 - August 2017

Intern - IFM Lab

Laboratoire d'Ingénierie des fonctions moléculaires (IFM Lab)
Institut de Sciences et d'Ingénierie Supramoléculaires (ISIS), UMR 7006
Université de Strasbourg, France

Description

Rescoring of docking results by end-point free energy approaches. Application to the Myosin molecular motor

Skills

  • Screening a library of compounds
  • Performing large-scale docking experiments
  • Scripting with bash and python 3
  • Running MD simulations with AmberTools and Amber:
    • Computing AM1-BCC charges with antechamber
    • Constructing topology and coordinates files with tLEaP
    • Submitting short simulations with sander and pmemd on multiple CPUs
    • Calculating binding free energies with MM/PBSA
  • Analyzing chemistry data
  • Implementing an algorithm from a publication to solve a problem
  • Launching calculations on a compute cluster
  • Communicating in English on a daily basis

Tools

  • Programming:
    • Shell: bash, awk, sed
    • Python: Jupyter-notebooks, pandas, numpy, scipy, rdkit, matplotlib, seaborn
  • Docking: PLANTS
  • Molecular Dynamics: Amber 16
  • Visualization: PyMOL, VMD
  • Job scheduler: PBS

Coworkers

Internship supervisor: Marco Cecchini
Members: Diego Enry Barreto Gomes, Nicolas Martin, Adrien Cerdan, Florian Blanc, Joel Montalvo Acosta
Interns: Paulina Pacak

March 2017 - June 2017

Intern - APSM Group

Aroma Perfume Synthesis and Modelling (APSM) Group
Institut de Chimie de Nice (ICN), Mixed research unit (UMR) 7272
Université Nice Sophia Antipolis, Nice, France

Description

Molecular modeling of bitter taste perception: sequence alignment, homology modelling, docking

Skills

  • Extracting data from publications
  • Constructing multiple sequence alignment of proteins
  • Creating homology models of proteins from sequence alignments
  • Running docking experiments

Tools

Coworkers

Internship supervisor: Sébastien Fiorucci
Members: Serge Antonczak, Jérôme Golebiowski, Jérémie Topin, Xiaojing Cong, Caroline Bushdid, Jean-Baptiste Chéron

June 2016

Summer jobs

Various banks in Monaco

Description

  • Summer replacement clerk, Compagnie Monégasque de Banque, Monaco, July 2016
  • Summer replacement clerk, BNP Paribas Wealth Management, Monaco, August 2015
  • Summer replacement teller, LCL Banque et Assurance, Monaco, July 2014
  • Summer replacement teller, LCL Banque et Assurance, Monaco, August 2013
  • Summer replacement teller, LCL Banque et Assurance, Monaco, July 2012

Skills

  • Greeting customers on site or by telephone
  • Handling sensible informations
  • Submitting banking transactions
  • Reorganizing folders and files

2012 - 2016