Leandro Oliveira Bortot

Leandro Oliveira Bortot Email and Phone Number

Data science | Machine Learning | Artificial Intelligence | Drug discovery | Quantitative finance | Cryptoassets @ Brazilian Center for Research in Energy and Materials (CNPEM)
campinas, sao paulo, brazil
Leandro Oliveira Bortot's Location
Campinas, São Paulo, Brazil, Brazil
About Leandro Oliveira Bortot

Have you ever wondered what it would be like if new planes were created through cycles of trial-and-error in which prototypes are built and tested "to see if it flies"? This is how drugs are developed today. I'm working with application, validation and development of computational methods that can contribute to a drug development process that is more data-driven and less dependent on trial-and-error cycles.  About 12 years ago I was presented to the fascinating problems that lie in the interfaces between biology, chemistry, physics and computation. Since then, I developed PhD and post-doctoral research projects that focus on drug discovery using computational methods. During this journey, I worked with dozens of biomolecular systems during collaborations that I established with several research groups. This experience allows me to adapt to changing environments and to promote effective communication in multidisciplinary teams, focusing on problem solving while balancing independent and collaborative work.  In addition to that, after delivering more than 30 presentations to diverse audiences, I can communicate complex concepts in a simple way according to the target audience.  I'm currently working in two main projects:    • Combining deep neural networks and molecular dynamics simulations to build models that can predict pharmacokinetic or toxicological properties of molecules that are candidates for new cosmetics or drugs. Such methods can reduce or even eliminate the necessity of animal testing in some instances.    • Planning, executing and analyzing virtual screening assays to discovery new drugs or to identify drugs that were approved against one disease that can potentially be used against other diseases. This approach, called "drug repositioning" or "drug repurposing", can lead to faster development of new therapies because the toxicological and pharmacokinetic profiles of approved drugs are already known.  I'm a specialist in learning and I'm always looking for new methods and tools to make my work better and more efficient, even if it requires learning subjects that I’m not familiar with. For now, these are my main technical skills:    • Machine learning and deep learning    • Data analysis    • Molecular dynamics simulations    • Docking-based virtual screening    • Structural bioinformatics    • Affinity/ΔG calculation

Leandro Oliveira Bortot's Current Company Details
Brazilian Center for Research in Energy and Materials (CNPEM)

Brazilian Center For Research In Energy And Materials (Cnpem)

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Data science | Machine Learning | Artificial Intelligence | Drug discovery | Quantitative finance | Cryptoassets
campinas, sao paulo, brazil
Website:
cnpem.br
Employees:
653
Leandro Oliveira Bortot Work Experience Details
  • Brazilian Center For Research In Energy And Materials (Cnpem)
    Scientific Computing Specialist I
    Brazilian Center For Research In Energy And Materials (Cnpem) Jan 2021 - Present
    Campinas, São Paulo, Brasil
    Responsible for the coordination, planning, execution and analysis of:  (i) virtual screening assays to identify molecules that have high potential of interacting with molecular targets that have therapeutical potential;  (ii) molecular dynamics simulations to solve problems related to the elucidation of ligand-receptor interaction modes or conformational changes.
  • Brazilian Center For Research In Energy And Materials (Cnpem)
    Postdoctoral Fellow
    Brazilian Center For Research In Energy And Materials (Cnpem) Apr 2019 - Dec 2020
    Campinas, São Paulo, Brasil
    • Implemented of an automated pipeline to execute, refine and analyze virtual screening assays that combines molecular dynamics simulations, docking and algorithms which were developed by our group (AutoDock Vina, AmberTools, GROMACS, Python, ArgParse, RdKit, OpenBabel, PyMOL). • Trained deep neural networks with data from molecular dynamics trajectories to build models that predict pharmacokinetic properties of drug candidate molecules (AmberTools, GROMACS, Python, SciKit-Learn, Keras, TensorFlow). • Trained more than 1 million neural network models to optimize its hyperparameters using parallel and distributed computing in clusters (Python, MultiProcessing, Jupyter NoteBooks, MatPloLlib, SeaBorn). • Obtained prediction error (RMSE and MSE) slightly smaller than the best model that was already published in the literature to predict pharmacokinetics properties of molecules that are drug or cosmetic candidates using deep neural networks with the fully connected and convolutional architectures (Python, NumPy, SKLearn, Keras/TensorFlow, RdKit, Mordred). • Mined an online database to build a dataset with more than 100,000 entries about toxicity of molecules (Python, BeautifulSoup4, Pandas).
  • University Of São Paulo
    Postdoctoral Researcher
    University Of São Paulo Jun 2018 - Feb 2019
    Ribeirão Preto, São Paulo, Brazil
    • Accelerated some structural analyzes that are performed by the research group by at least 16x using distributed computing (Python, MultiProcessing). • Accepted as Voluntary Teacher by Cursinho Popular Hypatia de Exatas (CPHE) from the Faculty of Philosophy, Sciences and Literature of Ribeirão Preto - University of São Paulo (FFCLRP -USP) after a teaching test and an interview. • Solved problems that the team was facing by performing structural bioinformatics analyzes of hundreds of 3D protein structures (Python, PyMOL). • Described the dynamic properties of new oligomeric forms of the human prion protein from a 3D structure that was determined by the research group under a novel crystallization condition (GROMACS).
  • University Of São Paulo
    Phd Student
    University Of São Paulo Feb 2013 - May 2018
    Ribeirão Preto, São Paulo, Brazil
    • Described the molecular mechanism for the recognition of glycosylated pathogens by a human receptor which is present in cells of the immune system. • Discovered an active molecule using computational drug repositioning. • Obtained R$ 247,000.00 (equivalent to U$ 61,750.00 – U$ 82,333.33 at the time) in grants. • Worked as Teaching Assistant for the “Physics I” undergraduate course which was part of the Pharmacy & Biochemistry undergraduate degree offered by the School of Pharmaceutical Sciences of Ribeirão Preto - University of São Paulo (FCFRP-USP). • Co-supervised one student of the Undergraduate Research Internship Institutional Program. • Collaborated as a member of a multinational team of 76 researchers dedicated to the protein structure prediction problem in 2016 (WeFold, CASP12). • Developed a method that uses structure-based criteria to select the most promising ligand-receptor complexes among 11.7 million possibilities generated by virtual screening.
  • Uppsala University
    Visiting Researcher
    Uppsala University Sep 2016 - Sep 2017
    Uppsala, Sweden
    • Employed three methods to calculate the interaction free energy (Umbrella Sampling, Jarzynski’s Equality and MM/PBSA) of a carbohydrate-lectin complex. • Modeled a heterogeneous biomolecular system with 1,5 million atoms that represents the bacterial cytoplasm and simulated its dynamics for 3 μs. • Used more than 1000 processing cores simultaneously with Beskow, the 61º fastest supercomputer of the world at the time. • Participated, as opponent, in a Master’s degree defense. • Validated a force field for membrane simulations with GROMACS.
  • School Of Pharmaceutical Sciences Of Ribeirão Preto
    Undergratuate Research Intern
    School Of Pharmaceutical Sciences Of Ribeirão Preto Aug 2008 - Dec 2012
    Ribeirão Preto, São Paulo, Brazil
    • Described the influence of different metals on the structural dynamics of a metalloprotein which is involved in the immune response.

Leandro Oliveira Bortot Education Details

Frequently Asked Questions about Leandro Oliveira Bortot

What company does Leandro Oliveira Bortot work for?

Leandro Oliveira Bortot works for Brazilian Center For Research In Energy And Materials (Cnpem)

What is Leandro Oliveira Bortot's role at the current company?

Leandro Oliveira Bortot's current role is Data science | Machine Learning | Artificial Intelligence | Drug discovery | Quantitative finance | Cryptoassets.

What schools did Leandro Oliveira Bortot attend?

Leandro Oliveira Bortot attended University Of São Paulo, Faculdade Focus, Etep - Centro Universitário, University Of São Paulo.

Who are Leandro Oliveira Bortot's colleagues?

Leandro Oliveira Bortot's colleagues are João Pedro Burle Ishida, Juliana Da Silva Bernardes, Isamara Rodrigues Barbosa, Simone Geisa Santos, Leticia Regina Martins Durello, Thaís Danilevicz, Ranieri Santos.

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