Erix W. Hernández Rodríguez

Departamento de Medicina Traslacional. Laboratorio de Bioinformática y Química Computacional (LBQC), Facultad de Medicina UCM

Línea de investigación: Fotofarmacología. Diseño racional de biocompuestos activos asistido por computadoras. Fotosensibilización y sistemas fotoactivos. Aplicación de métodos teórico-computacionales y modelos matemáticos en biomedicina.

Grado académico:

• Doctor en Medicina, Instituto Superior de Ciencias Médicas de La Habana, Cuba
• Especialista de Primer Grado en Bioquímica Clínica, Universidad de Ciencias Médicas de La Habana, Cuba
• Especialista de Segundo Grado en Bioquímica Clínica, Universidad de Ciencias Médicas de La Habana, Cuba
• Doctor en Ciencias Médicas (Área: Biomedicina), Universidad de Ciencias Médicas de La Habana, Cuba
• Doctor en Ciencias (Área: Química: Ciencia Interdisciplinar), Universidad Autónoma de Madrid, España
• Máster en Bioinformática, Instituto Superior de Tecnologías y Ciencias Aplicadas, Cuba

Publicaciones y Artículos:

• Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods. Bedoya, M., Adasme-Carreño, F., Peña-Martínez, P. A., Muñoz-Gutiérrez, C., Peña-Tejo, L., Montesinos, J. C. M., Hernández-Rodríguez E.W. González W., Martínez L., & Alzate-Morales, J. (2025).  Journal of Chemical Information and Modeling, 65(12), 5998-6013.  DOI: https://doi.org/10.1021/acs.jcim.5c00871 
• Natriuretic effect of 4′, 5-dihydroxy-6, 7-methylenedioxyflavonol-3-O-α-L-rhamnopyranosyl-(1→ 2)-β-D-xylopyranoside from Boldoa purpurascens: in silico and in vivo studies. Cañizares-Carmenate, Y., González-Mosquera, D. M., Perera-Sardiña, Y., Hernández-Rodríguez, E. W., Díaz-Amador, R., Castillo-Garit, J. A., & Tuenter, E.* (2024). Journal of Biomolecular Structure and Dynamics, 1-11. DOI: https://doi.org/10.1080/07391102.2024.2426075 
•  From proteome to potential drugs: integration of subtractive proteomics and ensemble docking for drug repurposing against Pseudomonas aeruginosa RND superfamily proteins. Urra, G., Valdés-Muñoz, E., Suardiaz, R., Hernández-Rodríguez, E. W., Palma, J. M., Ríos-Rozas, S. E., Flores-Morales, C.A., Alegría-Arcos, M., Yánez, O., Morales-Quintana, L., D´Afonseca, V., & Bustos, D. (2024). International Journal of Molecular Sciences, 25(15), 8027.  DOI: https://doi.org/10.3390/ijms25158027  
•  Unveiling novel urease inhibitors for Helicobacter pylori: a multi-methodological approach from virtual screening and ADME to molecular dynamics simulations. Valenzuela-Hormazabal, P., Sepúlveda, R. V., Alegría-Arcos, M., Valdés-Muñoz, E., Rojas-Pérez, V., González-Bonet, I., Suardíaz, R., Galarza, C., Morales, N., Leddermann, V., Castro, R.I., Benso, B., Urra, G., Hernández-Rodríguez, E. W., & Bustos, D. (2024). International Journal of Molecular Sciences, 25(4), 1968. DOI: https://doi.org/10.3390/ijms25041968  
• A description of the epidemiological dynamics of Chagas disease via mathematical modeling. Lozada-Yavina, R.*, Marchant, C., Cancino-Faure, B., Hernández-Rodríguez, E. W., & Córdova-Lepe, F. (2023). Acta Tropica, 243, 106930. DOI: https://doi.org/10.1016/j.actatropica.2023.106930 
• Calcium-alginate-chitosan nanoparticle as a potential solution for pesticide removal, a computational approach. Yáñez, O., Alegría-Arcos, M., Suardiaz, R., Morales-Quintana, L., Castro, R. I., Palma-Olate, J., Galarza, C., Catagua-González, A., Rojas-Pérez, V., Urra, G., Hernández-Rodríguez, E. W., & Bustos, D. (2023). Polymers, 15(14), 3020. DOI: https://doi.org/10.3390/polym15143020 
• Multi-omics data integration approaches for precision oncology. Correa-Aguila, R.*, Alonso-Pupo, N., & Hernandez-Rodriguez, E. W. (2022). Molecular Omics, 18(6), 469-479.  DOI: https://doi.org/10.1039/D1MO00411E 
• MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics. González-Alemán, R., Platero-Rochart, D., Rodríguez-Serradet, A., Hernández-Rodríguez, E. W., Caballero, J., Leclerc, F., & Montero-Cabrera, L. (2022). Bioinformatics, 38(23), 5191-5198. DOI: https://doi.org/10.1093/bioinformatics/btac666  
• BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics. González-Alemán, R., Platero-Rochart, D., Hernández-Castillo, D., Hernández-Rodríguez, E. W., Caballero, J., Leclerc, F., & Montero-Cabrera, L. (2022). Bioinformatics, 38(1), 73-79. DOI: https://doi.org/10.1093/bioinformatics/btab595 
• Canizares-Carmenate, Y., Mena-Ulecia, K., MacLeod Carey, D., Perera-Sardina, Y., Hernández-Rodríguez, E. W., Marrero-Ponce, Y., Torrens, F, & Castillo-Garit, J. A.* (2022). Machine learning approach to discovery of small molecules with potential inhibitory action against vasoactive metalloproteases. Molecular Diversity, 26(3), 1383-1397. DOI: https://doi.org/10.1007/s11030-021-10260-0 
• RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics. Platero-Rochart, D., González-Alemán, R., Hernández-Rodríguez, E. W., Leclerc, F., Caballero, J., & Montero-Cabrera, L. (2022). Bioinformatics, 38(7), 1863-1869. DOI: https://doi.org/10.1093/bioinformatics/btac021 
• Structural insights into the inhibition site in the phosphorylcholine phosphatase enzyme of Pseudomonas aeruginosa. Bustos, D., Hernández-Rodríguez, E. W., Poblete, H., Alzate-Morales, J., Challier, C., Boetsch, C., Vergara-Jaque, A., & Beassoni, P. (2022).. Journal of Chemical Information and Modeling, 62(12), 3067-3078. DOI: https://doi.org/10.1021/acs.jcim.2c00059 
• Structural Effects of pH variation and calcium amount on the microencapsulation of glutathione in alginate polymers. Bustos, D., Hernández-Rodríguez, E. W., Castro, R. I., & Morales-Quintana, L.* (2022).. BioMed Research International, 2022(1), 5576090. DOI: https://doi.org/10.1155/2022/5576090 
• Physicochemical and computational analysis of the melamine resin derivative for the glyphosate absorption from water using Langmuir-type model. Morales-Quintana, L., Bustos, D., Gallego, J., Valdes, O., Guzmán, L., Nachtigall, F. M., Marican, A., Hernández-Rodríguez, E. W., Ávila-Salas, F., Bueno-Silva, W., Santos, L.S., & Castro, R. I.* (2022). International Journal of Environmental Science and Technology, 19(8), 7791-7802.  DOI: https://doi.org/10.1007/s13762-021-03685-5 
• Brief tutorial to evaluate molecular cavities in large conformational ensembles: a K2P channel study case. Bustos, D.*, Palma-Olate, J.M., Vidal, M., González, W., Hernández-Rodríguez, E.W. (2021) IEEE International Conference on Automation/XXIV Congress of the Chilean Association of Automatic Control (ICA-ACCA). 2021-3-22. DOI: 10.1109/ICAACCA51523.2021.9465239 
• On the nature of the enzyme–substrate complex and the reaction mechanism in human arginase I. A combined molecular dynamics and QM/MM study. Velázquez-Libera, J. L., Caballero, J., Tunon, I., Hernández-Rodríguez, E. W.*, & Ruiz-Pernía, J. J. (2020). ACS Catalysis, 10(15), 8321-8333. DOI: https://doi.org/10.1021/acscatal.0c00981 
• Elucidating the structural basis of the intracellular pH sensing mechanism of TASK-2 K2P channels. Bustos, D., Bedoya, M., Ramírez, D., Concha, G., Zúñiga, L., Decher, N., Hernández-Rodríguez, E. W., Sepúlveda, F.V., Martínez, L., & González, W.* (2020). International Journal of Molecular Sciences, 21(2), 532. DOI: https://doi.org/10.3390/ijms21020532 
• Multi‐scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in rhodopsins. Hernández‐Rodríguez, E. W.*, Escorcia, A. M., Van Der Kamp, M. W., Montero‐Alejo, A. L., & Caballero, J. (2020). Journal of Computational Chemistry, 41(26), 2278-2295. DOI: https://doi.org/10.1002/jcc.26392
• Rationalizing the stability and interactions of 2, 4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2-hydroxy-3, 5-dinitrobenzoate salt. Tahir, M. N., Ashfaq, M., de la Torre, A. F., Caballero, J., Hernández-Rodríguez, E. W., & Ali, A. (2019). Journal of Molecular Structure, 1193, 185-194. DOI: https://doi.org/10.1016/j.molstruc.2019.05.003  
• BitClust: fast geometrical clustering of long molecular dynamics simulations. González-Alemán, R., Hernández-Castillo, D., Rodríguez-Serradet, A., Caballero, J., Hernández-Rodríguez, E. W., & Montero-Cabrera, L. (2019). Journal of Chemical Information and Modeling, 60(2), 444-448. DOI: https://doi.org/10.1021/acs.jcim.9b00828 
• Structure/Activity Analysis of TASK-3 Channel Antagonists Based on a 5, 6, 7, 8 tetrahydropyrido [4, 3-d] pyrimidine. Ramírez, D., Bedoya, M., Kiper, A. K., Rinné, S., Morales-Navarro, S., Hernández-Rodríguez, E.W., Sepúlveda, F.V., Decher, N., & González, W. (2019). International Journal of Molecular Sciences, 20(9), 2252. DOI: https://doi.org/10.3390/ijms20092252 
•  A study of the cis–trans isomerization preference of N-alkylated peptides containing phosphorus in the side chain and backbone. De la Torre, A. F., Ali, A., Concepcion, O., Montero-Alejo, A. L., Muñiz, F. M., Jiménez, C. A., Belmar, J, Velázquez-Libera, J.L., Hernández-Rodríguez, E.W. & Caballero, J. (2019). New Journal of Chemistry, 43(32), 12804-12813. DOI: https://doi.org/10.1039/C9NJ02234A  
• Panusin represents a new family of β-defensin-like peptides in invertebrates. Montero-Alejo, V., Corzo, G., Porro-Suardíaz, J., Pardo-Ruiz, Z., Perera, E., Rodríguez-Viera, L., Sánchez-Díaz, G.,  Hernández-Rodríguez, E.W., Álvarez, C., Peigneur, S., Tytgat, J., & Perdomo-Morales, R.* (2017). Developmental & Comparative Immunology, 67, 310-321.  DOI: https://doi.org/10.1016/j.dci.2016.09.002  
• Electron density deformations provide new insights into the spectral shift of rhodopsins. Hernández‐Rodríguez, E. W., Montero‐Alejo, A. L., López, R., Sánchez‐García, E., Montero‐Cabrera, L. A., & García de la Vega, J. M.* (2013). Journal of Computational Chemistry, 34(28), 2460-2471. DOI: https://doi.org/10.1002/jcc.23414  
• Understanding rhodopsin mutations linked to the retinitis pigmentosa disease: a QM/MM and DFT/MRCI study. Hernández-Rodríguez, E. W., Sánchez-García, E.*, Crespo-Otero, R., Montero-Alejo, A. L., Montero, L. A., & Thiel, W. (2012). The Journal of Physical Chemistry B, 116(3), 1060-1076. DOI: https://doi.org/10.1021/jp2037334  
• Defensin like peptide from Panulirus argus relates structurally with beta defensin from vertebrates. Montero-Alejo, V.*, Acosta-Alba, J., Perdomo-Morales, R., Perera, E., Hernández-Rodríguez, E.W., Estrada, M. P., & Porto-Verdecia, M. (2012). Fish & shellfish immunology, 33(4), 872-879. DOI: https://doi.org/10.1016/j.fsi.2012.07.013  
• Validations of CNDOL approximate Hamiltonian as a fast and reliable method to obtain vertical excitation energies in polyatomic systems. Montero-Alejo, A. L.*, Gonzalez-Santana, S., Montero-Cabrera, L. A., Hernández-Rodríguez, E.W., Fuentes-Montero, M. E., Bunge-Molina, C. F., & Gonzalez, A. (2008). Acceso en: https://www.osti.gov/etdeweb/biblio/22005040  
• Patterns of retinal light absorption related to retinitis pigmentosa mutants from in silico model structures of rhodopsin. Padrón‐García, J. A., Crespo‐Otero, R., Hernández-Rodríguez, E.W., Garriga, P., Montero, L. A.*, & García‐Piñeiro, J. C. (2004). Proteins: Structure, Function, and Bioinformatics, 57(2), 392-399. DOI: https://doi.org/10.1002/prot.20204