I have focused my career on computational tools for the analysis of biomolecular systems. My projects are strongly related to molecular modelling, simulations of protein dynamics and protein-ligand interactions, including steered molecular dynamics and free energy landscape calculations. However, I have also participated in other projects for the analysis (and/or code developing for the analysis) of genetic, biochemical, and chemical data. Including approaches of machine and deep learning as well as bio- and chemo- informatics.
Display standard CVGROMACS, MDAnalysis, VMD, Chimera UCSF, AutoDock VINA, CB-Dock, MGLTools, PyMol, Rosetta software, AlphaFold, RFdiffusion, LIGPLOT, swiss-model, Avogadro, BIOVIA
GenBank, Biopython, EMBL-tools, PROSITE, T-coffe, Rdkit, Openbabel, Numpy, Pandas, Matplotlib, Seaborn, Plotly, Scikit-learn, Pytorch
Python, R, Bash-Scripting, VIM, tmux (LINUX/UNIX)
[Research article, First Author]
Herrera-Rodulfo, A., Andrade-Medina, M., García-Delgado, M.S., & Carrillo-Tripp, M. (In Press, 2025).
Extensive In-silico Target-Ligand Conformational Space Sampling of Garlic-Derived Sulfur Compounds Targeting COVID-19 Infection.
Journal of Computational Biophysics and Chemistry.
[Research article, Co-Author]
Granados-Tristán, A. L., Carrillo-Tripp, M., Hernández-Luna, C. E., Herrera-Rodulfo, A., González-Escalante, L. A., Arriaga-Guerrero, A. L., Silva-Ramírez, B., Escobedo-Guajardo, B. L., Mercado-Hernández, R., Bermúdez de León, M., & Peñuelas-Urquides, K. (In Press, 2025).
Mycobacterium Susceptibility to Ivermectin by Inhibition of eccD3, an ESX-3 Secretion System Component.
PLOS Computational Biology.
[Peer-reviewed Book Chapter, First Author]
Herrera-Rodulfo, A., Andrade-Medina, M., & Carrillo-Tripp, M. (2022).
Repurposing Drugs as Potential Therapeutics for the SARS-CoV-2 Viral Infection: Automatizing a Blind Molecular Docking High-throughput Pipeline.
In Biomedical Engineering. IntechOpen.
https://doi.org/10.5772/intechopen.105792
(Free pipeline available on GitHub).
[Review Article, Co-Author]
del Rayo Camacho-Corona, M., Camacho-Morales, A., Góngora-Rivera, F., Escamilla-García, E., Morales-Landa, J. L., Andrade-Medina, M., Herrera-Rodulfo, A., García-Juárez, M., García-Espinosa, P., Stefani, T., González-Barranco, P., & Carrillo-Tripp, M. (2022).
Immunomodulatory Effects of Allium sativum L. and its Constituents Against Viral Infections and Metabolic Diseases.
Current Topics in Medicinal Chemistry, 22(2), 109–131.
https://doi.org/10.2174/1568026621666211122163156.
[Research Article, First Author]
Herrera-Rodulfo, A., Carrillo-Tripp, M., Laura Yeverino-Gutierrez, M., Peñuelas-Urquides, K., Adiene González-Escalante, L., Bermúdez de León, M., & Silva-Ramirez, B. (2021).
NAT2 Polymorphisms Associated with the Development of Hepatotoxicity After First-line Tuberculosis Treatment in Mexican Patients: From Genotype to Molecular Structure Characterization.
Clinica Chimica Acta, 519, 153–162.
https://doi.org/10.1016/j.cca.2021.04.017.
[Research Article, First Author]
The Role of Conformational Dynamics Conservation in the Structure-Function Paradigm: A Case Study on the RBD of SARS-CoV-2 Spike Protein Variants.
In preparation.
[Research Article, First Author]
Drug-Target Interaction Miner: A Computational Framework for Protein-Ligand Interaction Analysis Using Modern Artificial Intelligence Architectures and Graph Theory.
In preparation.
[Research Article, Co-Author]
High-Throughput Virtual Screening of Organosulfur Compounds Targeting SARS-CoV-2 Spike Protein: In Silico and In Vitro Analysis.
In preparation.
>PhD in Engineering and Biomedical Physics.
Biomolecular Diversity Lab at the Center for Research and Advanced Studies (CINVESTAV). 2020-2024.
>Master in science focused on pharmacy.
Immunogenetics lab at Northeast Biomedical Research Center (CIBIN, IMSS) and the Faculty of Chemistry at Autonomous University of Nuevo León (FCQ, UANL). 2018-2020
>Bachelor in chemistry applied to biological and pharmaceutical sciences.
Faculty of Chemistry at Autonomous University of Nuevo León (UANL). 2013-2018
>Research stay on deep learning graph-neural networks and honored to be awarded the HIDA's Helmholtz Visiting Researcher Grant.
Research stay in the Drug Bioinformatics group at Helmholtz Institute for Pharmaceutical Research Saarland (WIBI, HIPS). Saarbrücken, Germany - 2023
>Practical and theoretical course on molecular modelling and dynamics
Research stay at Biomolecular diversity group at Center for Research and Advance Studies (CINVESTAV). Monterrey, México - 2019
>Undergrad Research Experience
Undergrad research internship at a laboratory dedicated to research on organic synthesis of compounds with potential pharmacological activity at the Faculty of Chemistry at Autonomous University of Nuevo León (FCQ, UANL).I also enjoy participating in activities related to teaching science and divulgation. Here I’ll list a few projects that I was lucky to be part of.
>Who stole the virus? | I helped to solve a mystery at the BMD lab. I have participated in two editions (2022 and 2023) of "Who stole the virus?". A didactic course that employs in-vitro and in-silico tools to solve a well-planned mystery by master's students of the master program in biology education for citizen formation at the Center of Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN). My contribution includes day-to-day consulting and conferences and workshops on bioinformatic analysis of genomic sequences. >How small a virus is? | How do students perceive the size of small entities?. Sometimes the size of the biological world is not as intuitive as we think. I was part of a team that help out high-school students to deeper understand how small entities are more fun than they thought, we used audiovisuals, graphic storyboards, paper virus models at the week of science, art and technology at Roberto Rocca technical school (8 and 9 of June 2022) in a workshop named: “A trial to a virus: the small and the very small”. >What motivated me to do science? | I shared my experience with the future teachers of biology students. I was invited as a member of the Biomolecular Diversity Lab to share my experience as a science student. I share my motivations to do science, and what I enjoy about it. Then, I also helped the project-leaders to analyze the results of this course (throughout biology trainee teachers drawings!). This was part of a course of nature of sciences at the benemerit and centenary school for future teachers of Jalisco (ByCENJ).