Pablo R. Arantes

Research scientist at the University of California




About Me



My name is Pablo Ricardo Arantes, I am a research scientist at the University of California Riverside, working in the field of biophysics (Palermo Lab). I hold extensive expertise in computational biophysics and knowledge in state‐ of‐the‐art computational methods that have been proven instrumental in delving deep into biological function.

My research at the University of California focuses on molecular simulations of emerging genome editing technologies based on the CRISPR‐Cas9 system that received the Nobel Prize of Chemistry 2020.

In 2021, I have worked on the first user‐friendly front‐end for running molecular dynamics (MD) simulations using the OpenMM toolkit on the Google Colab framework (Making it rain). An affordable (cost‐free) strategy for performing molecular dynamics simulations using cloud computing resources. It involves shareable, ready‐to‐use, customizable Jupyter notebooks that guide the end‐user in running their calculations using Google Colab services.

My current collaboration network includes biochemists, bioinfomaticians, and structural biologists from Brazil, Uruguay, England, Spain, Australia and USA.


Education


PhD in Cellular & Molecular Biology

  • 2014 - 2018
  • Federal University of Rio Grande do Sul - Porto Alegre - Brazil
  • Structural and Dynamic Bases of Biomolecules on the N‐glycosylation pathway in Bacteria
  • Advisor: Dr. Hugo Verli
  • Scholarship from: CNPq and CAPES

 

Education


Master's in Cellular & Molecular Biology

  • 2013 - 2014
  • Federal University of Rio Grande do Sul - Porto Alegre - Brazil
  • Force Fields Reliability on the Description of protein complexed and uncomplexed siRNA
  • Advisor: Dr. Hugo Verli
  • Scholarship from: CNPq and CAPES

 

Education


Bachelor's in Pharmaceutical Sciences

  • 2007 - 2012
  • Federal University of Rio Grande do Sul - Porto Alegre - Brazil
  • Advisor: Dr. Hugo Verli
  • Scholarship from: CNPq and CAPES

 

Experiences


Postdoctoral Researcher

  • 2019 – Current
  • University of California, Riverside
  • Position: Postdoctoral Researcher under Dr. Giulia Palermo
  • Activities: Structural and conformational characterization of of proteins and nucleic acids involved in genome editing and regulation, which are promising against cancer and genetic diseases. Please, see more information here.

 

Experiences


Research Fellow

  • 2018 – 2019
  • Federal University of Health Sciences of Porto Alegre - Brazil
  • Activities: Structural and conformational characterization of Nek1 protein and new pyrimidine inhibitors with therapeutic potential in the treatment of glioblastoma.
  • Supervisor: Dr. Dinara Jaqueline Moura

 

Projects


Making it rain

  • Making it rain is a Jupyter notebook scripts for running Molecular Dynamics (MD) simulations using OpenMM engine and AMBER and CHARMM force fields files on Google Colab. The main goal of this work is to demonstrate how to harness the power of cloud-computing to run microsecond-long MD simulations in a cheap and yet feasible fashion. More information here: Making-it-rain.

 

Projects


Cloud-Bind

  • Cloud-Bind is a repository where you can find a Jupyter notebook scripts for running GNINA (molecular docking program with integrated support for scoring and optimizing ligands using convolutional neural networks), Uni-Dock (GPU-accelerated molecular docking program) and OpenBPMD (evaluating ligand pose stability using metadynamics) on Google Colab. More information here: Cloud-Bind.

 

Projects


ParametrizANI

  • ParametrizANI is a repository where you can find a Jupyter notebook scripts to set up a protocol for parametrization of small molecules dihedrals using TorchANI as a reference, a PyTorch-based program for training/inference of ANI (ANAKIN-ME) deep learning models to obtain potential energy surfaces and other physical properties of molecular systems. More information here: ParametrizANI.

 

Publications


List of Publications