Ricardo Ramirez

Background

About Ricardo Ramirez

I am interested in the computational modeling of biological systems. My current research is devoted to studying the interaction between proteins and lipids through all-atom molecular dynamics (MD). This work involves the use of different software such as GROMACS to simulate macromolecular systems that contain near to atoms (usually including proteins, lipid bilayer, water, and ions). I have expertise in setting up these types of molecular systems: initialization of protein structures, post-translational modifications, merging different structures, solvation, protonation, minimization, and equilibration. For the analysis of the trajectories, I have experience in computing hydrogen bonds, tilt angles, Markov state models, and binding conformations. I am also interested in applying machine learning techniques to analyze various aspects of these molecular systems. I am convinced that Deep Learning can be helpful to further explore this kind of system, even in the structural part with Alphafold or the docking part with the Alphafold-multimer of Equibind.Other of my interest include quantum computing, for which I participated in the quantum challenge 2020 and got an advanced badge for applying quantum circuits to solving proposed problems.