Mariana Gonzalez Medina

Paris · mgm14392@gmail.com

Passionate about chemistry, drug discovery and artificial intelligence. I am currently finishing a PhD in bioinformatics at the Institut Pasteur in Paris with a scholarship from the INCEPTION program. I have 5 years of experience on chemoinformatics and 3 years of experience on machine learning, and protein modeling. As a next step of my professional career, I am thrilled to develop those expertises by joining a fast-paced and innovative company with a focus on the development of algorithms for drug discovery, precision medicine or protein modeling.

Projects / Publications / Talks

Junior researcher

Institut Pasteur

Comparative modeling of a nicotinic receptor in a resting, activated and desensitized conformation. (MODELLER | python)

Transition path sampling between conformations. Cavity analysis on the transition path. (GROMACS | CHARMM)

Cavity clustering and de novo drug desing on interesting cavities. (PyTorch | Tensorflow)

Pipeline for synthetic feasibility for compounds from the novo drug design. (rdkit | PyTorch)

September 2019 - December 2022

Student assistant

Bonn b-it

Web scraping, PDF parsing, data curation and organization of the biological activity of compounds assayed as kinase inhibitors. (python)

Graph analysis and visualization of structure activity relationships (SAR). Published paper. (Python | Cytoscape | R)

January 2019 - August 2019

Student assistant

UNAM

Development of PUMA, online web application to do visualize the chemical space as well as the structural and chemical properties diversity analysis of compound databases. Shiny code (R | shiny | rcdk)

Development of AL Plotter, online web application to do visualize activity cliffs and do structure activity relationships. Shiny code (R | shiny | rcdk)

Development of CD Plots, online web application to compare the structural and molecular properties diversity of several databases. (R | shiny | rcdk)

December 2016 - June 2017

Publications

All publications can be found on Google Scholar.

Talks

Modeling of the a4a5b2 nicotinic receptor. Inception Annual Meeting. Institut Pasteur. Paris, France. November 25, 2022.

Consensus Diversity Plots LS2 Satellite Meeting. Frontiers in Medicinal Chemistry. Bern, Switzerland. February 12-15, 2017.

Education

Universite Paris Cite

PhD. Structural Bioinformatics
Modeling and structural analysis of the α4α5β2 nicotinic acetylcholine receptor (nAchR)
September 2019 - December 2022

Bonn-Aachen International Center for Information Technology

M.Sc. Life Science Informatics
Biological activity curation, organization and analysis of kinase inhibitors from medicinal chemistry
October 2017 - August 2019

Universidad Nacional Autonoma de Mexico

B.Sc. Chemistry and Pharmacy
Chemoinformatic expedition of the chemical space of fungal products
August 2011 - December 2016

Skills

Programming Languages & Tools
  • Shell Scripting and Linux Architecture
  • Experience with relational databases MySQL
  • R: ggplot2, Plotly, rcdk, shiny, dplyr (...)
  • Python: rdkit, openbabel, Pandas, Numpy, PyTorch, SciPy, Plotly, Scikit-Learn, Matplotlib (...)
  • HPC system: SLURM scheduler
  • REST Services and API
  • Version control systems: GitHub
  • Deployment technologies: Docker

Drug design skills
  • Molecular properties, fingerprint calculation, similarity searching, structural diversity analysis. (rdkit | rcdk | openbabel)
  • Protein modeling. (MODELLER | Rosetta Commons | GROMACS | pymol | VMD | HOLE | reduce | Maestro)
  • Virtual screening and library preparation. (AutoDock | MGLTools | smina)
  • De novo drug design. (PyTorch | Ligmolgrid | rdkit | tensorboard)

Languages
  • Spanish native speaker
  • English C2
  • French B1
  • German A2

Interests

My extremely cute dog, swimming, reading, beer and horror films.

Awarded Scholarships

  • Scholarship for PhD degree at Institut Pasteur. PPU-Inception (01/10/2019- 01/09/2022
  • Scholarship for Master’s degree. CONACyT-FUNED 660673 (01/10/2017- 01/10/2019)
  • Scholarship for Bachelor’s thesis research project. PAPIME PE200116 (UNAM) (03/2016-12/2016)
  • Scholarship from Secretaría de Educación Pública (SEP) for exchange program at Masaryk University, Czech Republic (09/2015-02/2016)
  • Scholarship from Mitacs for Globalink Research Internship (GRI) at the University of New Brunswick, Canada (06/2015 – 08/2015)
  • Scholarship from COMEXUS-SEP (FOBESII) for Research Experience for Undergraduates (REU) at the University of California Davis, United States of America (06/2014 – 08/2014)