Bioquímica Farmacológica — Computational Lab
Molecular docking practical: GNINA workshop and docking simulation notebooks.
Posts by Collection
portfolio
Biología Molecular de Sistemas — Class Material
Course material for a Systems Biology module.
Graph Neural Networks: Understanding Network Data with Deep Learning
Interactive teaching module on GNNs for systems biology, with notebook, article and audio overview.
Mapa de Profesiones
Career-orientation guide for pre-university students: from bachillerato to profession.
Directional allosteric communication in protein language model attention
Analysis code for the ESM-2 attention-asymmetry study of the adenosine A2A receptor (bioRxiv 2026).
ESM Allostery Analysis
Identifying which ESM-2 attention heads are most sensitive to known allosteric sites.
PLMs Dynamic Allostery
Extracting allostery-sensitive attention heads from ESM-2 and computing per-residue allostery scores.
Protein Structure Network
Centrality of amino acids in a protein structure network derived from normal mode analysis.
publications
Local changes in the catalytic site of mammalian histidine decarboxylase can affect its global conformation and stability
Published in European Journal of Biochemistry, 2003
Recommended citation: Rodríguez‐Caso C., Rodríguez‐Agudo D., Moya‐García A.A., et al. (2003). "Local changes in the catalytic site of mammalian histidine decarboxylase can affect its global conformation and stability." European Journal of Biochemistry. 270(21). 4376-4387.
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Mapping of catalytically important residues in the rat L-histidine decarboxylase enzyme using bioinformatic and site-directed mutagenesis approaches
Published in Biochemical Journal, 2004
Recommended citation: FLEMING J.V., SÁNCHEZ-JIMÉNEZ F., MOYA-GARCÍA A.A., LANGLOIS M.R., WANG T.C. (2004). "Mapping of catalytically important residues in the rat L-histidine decarboxylase enzyme using bioinformatic and site-directed mutagenesis approaches." Biochemical Journal. 379(2). 253-261.
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Mammalian histidine decarboxylase: from structure to function
Published in BioEssays, 2005
Recommended citation: Moya-Garcia A.A., Medina M.Á., Sánchez-Jiménez F. (2005). "Mammalian histidine decarboxylase: from structure to function." BioEssays. 27(1). 57-63.
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New structural insights to help in the search for selective inhibitors of mammalian pyridoxal 5′-phosphate-dependent histidine decarboxylase
Published in Inflammation Research, 2006
Recommended citation: Sánchez-Jiménez F., Moya-García A.A., Pino-Ángeles A. (2006). "New structural insights to help in the search for selective inhibitors of mammalian pyridoxal 5′-phosphate-dependent histidine decarboxylase." Inflammation Research. 55(S1). S55-S56.
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AMMO-Prot: amine system project 3D-model finder
Published in BMC Bioinformatics, 2008
Recommended citation: Navas-Delgado I., Montañez R., Pino-Ángeles A., et al. (2008). "AMMO-Prot: amine system project 3D-model finder." BMC Bioinformatics. 9(S4).
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Analysis of the decarboxylation step in mammalian histidine decarboxylase. A computational study
Published in Journal of Biological Chemistry, 2008
Recommended citation: Moya-García A.A., Ruiz-Pernía J., Martí S., Sánchez-Jiménez F., Tuñón I. (2008). "Analysis of the decarboxylation step in mammalian histidine decarboxylase. A computational study." Journal of Biological Chemistry. 283(18). 12393-12401.
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Study by optical spectroscopy and molecular dynamics of the interaction of acridine-spermine conjugate with DNA
Published in Biophysical Chemistry, 2008
Recommended citation: Sánchez-Carrasco S., Delcros J., Moya-García A., Sánchez-Jiménez F., Ramírez F. (2008). "Study by optical spectroscopy and molecular dynamics of the interaction of acridine-spermine conjugate with DNA." Biophysical Chemistry. 133(1-3). 54-65.
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Molecular modeling and site-directed mutagenesis reveal essential residues for catalysis in a prokaryote-type aspartate aminotransferase
Published in Plant Physiology, 2009
Recommended citation: de la Torre F., Moya-García A.A., Suárez M., et al. (2009). "Molecular modeling and site-directed mutagenesis reveal essential residues for catalysis in a prokaryote-type aspartate aminotransferase." Plant Physiology. 149(4). 1648-1660.
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Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition
Published in British Journal of Pharmacology, 2009
Recommended citation: Moya‐García A., Pino‐Ángeles A., Gil‐Redondo R., Morreale A., Sánchez‐Jiménez F. (2009). "Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition." British Journal of Pharmacology. 157(1). 4-13.
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Digitalis purpurea P5βR2, encoding steroid 5β-reductase, is a novel defense-related gene involved in cardenolide biosynthesis
Published in New Phytologist, 2010
Recommended citation: Pérez‐Bermúdez P., Moya García A.A., Tuñón I., Gavidia I. (2010). "Digitalis purpurea P5βR2, encoding steroid 5β-reductase, is a novel defense-related gene involved in cardenolide biosynthesis." New Phytologist. 185(3). 687-700.
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Molecular characterization of five patients with homocystinuria due to severe methylenetetrahydrofolate reductase deficiency
Published in Clinical Genetics, 2010
Recommended citation: Urreizti R., Moya‐García A., Pino‐Ángeles A., et al. (2010). "Molecular characterization of five patients with homocystinuria due to severe methylenetetrahydrofolate reductase deficiency." Clinical Genetics. 78(5). 441-448.
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Substrate uptake and protein stability relationship in mammalian histidine decarboxylase
Published in Proteins: Structure, Function, and Bioinformatics, 2010
Recommended citation: Pino‐Ángeles A., Morreale A., Negri A., Sánchez‐Jiménez F., Moya‐García A.A. (2010). "Substrate uptake and protein stability relationship in mammalian histidine decarboxylase." Proteins: Structure, Function, and Bioinformatics. 78(1). 154-161.
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Analysis of mammalian histidine decarboxylase dimerization interface reveals an electrostatic hotspot important for catalytic site topology and function
Published in Journal of Chemical Theory and Computation, 2011
Recommended citation: Moya-García A.A., Rodríguez-Agudo D., Hayashi H., Medina M.A., Urdiales J.L., Sánchez-Jiménez F. (2011). "Analysis of mammalian histidine decarboxylase dimerization interface reveals an electrostatic hotspot important for catalytic site topology and function." Journal of Chemical Theory and Computation. 7(6). 1935-1942.
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Enzymology in histamine biogenesis
Published in Biomedical Aspects of Histamine, 2011
Recommended citation: Pino-Ángeles A., Moya-García A.A., Medina M.Á., Sánchez-Jiménez F. (2011). "Enzymology in histamine biogenesis." Biomedical Aspects of Histamine. 33-57.
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The function of histamine receptor H4R in the brain revealed by interaction partners
Published in Frontiers in Bioscience, 2011
Recommended citation: Moya-Garcia A.A. (2011). "The function of histamine receptor H4R in the brain revealed by interaction partners." Frontiers in Bioscience. S3(3). 1058-1066.
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Structural perspective on the direct inhibition mechanism of EGCG on mammalian histidine decarboxylase and DOPA decarboxylase
Published in Journal of Chemical Information and Modeling, 2012
Recommended citation: Ruiz-Pérez M.V., Pino-Ángeles A., Medina M.A., Sánchez-Jiménez F., Moya-García A.A. (2012). "Structural perspective on the direct inhibition mechanism of EGCG on mammalian histidine decarboxylase and DOPA decarboxylase." Journal of Chemical Information and Modeling. 52(1). 113-119.
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Bicyclic derivatives of L-idonojirimycin as pharmacological chaperones for neuronopathic forms of Gaucher disease
Published in ChemBioChem, 2013
Recommended citation: Alfonso P., Andreu V., Pino‐Angeles A., et al. (2013). "Bicyclic derivatives of L-idonojirimycin as pharmacological chaperones for neuronopathic forms of Gaucher disease." ChemBioChem. 14(8). 943-949.
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Insights into polypharmacology from drug-domain associations
Published in Bioinformatics, 2013
Recommended citation: Moya-García A.A., Ranea J.A.G. (2013). "Insights into polypharmacology from drug-domain associations." Bioinformatics. 29(16). 1934-1937.
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Aminooxy analog of histamine is an efficient inhibitor of mammalian l-histidine decarboxylase: Combined in silico and experimental evidence
Published in Amino Acids, 2014
Recommended citation: Castro-Oropeza R., Pino-Ángeles A., Khomutov M.A., et al. (2014). "Aminooxy analog of histamine is an efficient inhibitor of mammalian l-histidine decarboxylase: Combined in silico and experimental evidence." Amino Acids. 46(3). 621-631.
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Biocomputational resources useful for drug discovery against compartmentalized targets
Published in Current Pharmaceutical Design, 2014
Recommended citation: Sanchez-Jimenez F., Reyes-Palomares A., Moya-Garcia A., Ranea J., Medina M. (2014). "Biocomputational resources useful for drug discovery against compartmentalized targets." Current Pharmaceutical Design. 20(2). 293-300.
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Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies
Published in Oncotarget, 2016
Recommended citation: Bueno A., Morilla I., Diez D., Moya-Garcia A.A., Lozano J., Ranea J.A. (2016). "Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies." Oncotarget. 7(46). 75810-75826.
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Structural and Functional View of Polypharmacology
Published in Scientific Reports, 2017
Recommended citation: Moya-García A., Adeyelu T., Kruger F.A., et al. (2017). "Structural and Functional View of Polypharmacology." Scientific Reports. 7(1).
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Unique signalling connectivity of FGFR3-TACC3 oncoprotein revealed by quantitative phosphoproteomics and differential network analysis
Published in Oncotarget, 2017
Recommended citation: Lombardi B., Ashford P., Moya-Garcia A.A., et al. (2017). "Unique signalling connectivity of FGFR3-TACC3 oncoprotein revealed by quantitative phosphoproteomics and differential network analysis." Oncotarget. 8(61). 102898-102911.
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A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations
Published in Scientific Reports, 2019
Recommended citation: Ashford P., Pang C.S.M., Moya-García A.A., Adeyelu T., Orengo C.A. (2019). "A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations." Scientific Reports. 9(1).
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Histamine, metabolic remodelling and angiogenesis: A systems level approach†
Published in Biomolecules, 2021
Recommended citation: Moya-García A.A., Pino-Ángeles A., Sánchez-Jiménez F., Urdiales J.L., Medina M.Á. (2021). "Histamine, metabolic remodelling and angiogenesis: A systems level approach†." Biomolecules. 11(3). 415.
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A course-based undergraduate research experience to illustrate the early stages of the drug discovery process
Published in Biochemistry and Molecular Biology Education, 2022
Recommended citation: García‐Caballero M., Moya‐García A., Torres‐Vargas J.A., García‐Ponce Á.L., Rodríguez‐Quesada A. (2022). "A course-based undergraduate research experience to illustrate the early stages of the drug discovery process." Biochemistry and Molecular Biology Education. 50(5). 437-439.
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Exploiting protein family and protein network data to identify novel drug targets for bladder cancer
Published in Oncotarget, 2022
Recommended citation: Adeyelu T.T., Moya-Garcia A.A., Orengo C. (2022). "Exploiting protein family and protein network data to identify novel drug targets for bladder cancer." Oncotarget. 13(1). 105-117.
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Genes Involved in Immune Reinduction May Constitute Biomarkers of Response for Metastatic Melanoma Patients Treated with Targeted Therapy
Published in Biomedicines, 2022
Recommended citation: Berciano-Guerrero M., Lavado-Valenzuela R., Moya A., et al. (2022). "Genes Involved in Immune Reinduction May Constitute Biomarkers of Response for Metastatic Melanoma Patients Treated with Targeted Therapy." Biomedicines. 10(2). 284.
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Identification of New Toxicity Mechanisms in Drug-Induced Liver Injury through Systems Pharmacology
Published in Genes, 2022
Recommended citation: Moya-García A.A., González-Jiménez A., Moreno F., Stephens C., Lucena M.I., Ranea J.A.G. (2022). "Identification of New Toxicity Mechanisms in Drug-Induced Liver Injury through Systems Pharmacology." Genes. 13(7). 1292.
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Role of germline variants in the metastasis of breast carcinomas
Published in Oncotarget, 2022
Recommended citation: Santonja Á., Moya-García A.A., Ribelles N., et al. (2022). "Role of germline variants in the metastasis of breast carcinomas." Oncotarget. 13(1). 843-862.
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KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units
Published in Biomolecules, 2023
Recommended citation: Adeyelu T., Bordin N., Waman V.P., et al. (2023). "KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units." Biomolecules. 13(2). 277.
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Better understanding the phenotypic effects of drugs through shared targets in genetic disease networks
Published in Frontiers in Pharmacology, 2024
Recommended citation: Díaz-Santiago E., Moya-García A.A., Pérez-García J., et al. (2024). "Better understanding the phenotypic effects of drugs through shared targets in genetic disease networks." Frontiers in Pharmacology. 15.
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Topological attention asymmetry in ESM-2 attention implicitly encodes the allosteric hierarchy of the adenosine A2A receptor
Published in bioRxiv, 2026
Recommended citation: Moya-García A.A. (2026). "Topological attention asymmetry in ESM-2 attention implicitly encodes the allosteric hierarchy of the adenosine A2A receptor." bioRxiv.
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talks
teaching
Biofísica
Asignatura de grado (2º curso, obligatoria, 6 ECTS) — Grado en Bioquímica, Universidad de Málaga, Facultad de Ciencias, 2025
Fundamentos físicos de los sistemas biológicos: termodinámica de organismos vivos, estructura supramolecular y autoensamblaje, difusión y permeabilidad de membranas, mecanismos de transporte, máquinas moleculares, dinámica biomolecular, transducción de señales y sistemas de memoria biológica.
Bioquímica e Ingeniería de Proteínas
Asignatura de grado — Grado en Bioquímica, Universidad de Málaga, Facultad de Ciencias, 2025
Curso de aprendizaje basado en proyectos (PBL, siguiendo los principios de Finkel y del modelo de Aalborg) sobre estructura, plegamiento, estabilidad y diseño computacional de proteínas. El componente práctico central usa notebooks de Jupyter con PyRosetta para manipulación de estructuras, funciones de scoring, simulación de plegamiento y diseño racional de proteínas.
Bioquímica
Asignatura de grado — Grado en Química, Grado en Bioquímica, Universidad de Málaga, Facultad de Ciencias, 2025
Asignatura de Bioquímica con enfoque socrático centrado en la lógica metabólica antes que en la memorización de rutas. Introducción al metabolismo, bioenergética (termodinámica y transportadores de ATP), glucólisis/gluconeogénesis y metabolismo del glucógeno, metabolismo del piruvato y complejo PDH, catabolismo de aminoácidos y ciclo de la urea, e integración del metabolismo en mamíferos.
Estructura de Macromoléculas
Asignatura de grado (2º curso, obligatoria, 6 ECTS) — Grado en Bioquímica, Universidad de Málaga, Facultad de Ciencias, 2025
Análisis teórico y experimental de las propiedades físicas y químicas de las macromoléculas biológicas (proteínas y ácidos nucleicos), organizado en tres bloques: técnicas de análisis estructural espectroscópicas y no espectroscópicas; estructura, estabilidad, plegamiento y reconocimiento de proteínas; y estructura de ácidos nucleicos e interacciones proteína-ácido nucleico.
Herramientas y Algoritmos en Bioinformática
Asignatura de grado (4º curso) — Grado en Bioquímica, Universidad de Málaga, Facultad de Ciencias, 2025
Laboratorio computacional de bioinformática centrado en análisis funcional (conversión de identificadores génicos, enriquecimiento de rutas y redes) y algoritmos de propagación de redes (“network propagation”). Los estudiantes completan tareas prácticas progresivas que culminan en un proyecto final que integra ambos enfoques sobre un caso de análisis funcional real.
Biología Molecular del Cáncer — Seminario: IA en Investigación Oncológica
Seminario de aprendizaje activo (4º curso) — Grado en Bioquímica, Universidad de Málaga, Facultad de Ciencias, 2026
Seminario de tres horas que emplea IA generativa como herramienta de exploración crítica sobre controversias abiertas en biología del cáncer (enfermedad genética frente a metabólica, células madre tumorales, SMT frente a TOFT, paradoja de Peto, nicho premetastásico, heterogeneidad intratumoral). Los estudiantes diseñan pipelines de aprendizaje automático para datos transcriptómicos y después someten el razonamiento de la IA a escrutinio sistemático.