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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
About Me
About me
Posts
A Pipeline for Structure-Aware Docking
Published:
One UniProt Code, Many Conformations, Zero Excuses: A Pipeline for Structure-Aware Docking
portfolio
Portfolio item number 1
Published:
Short description of portfolio item number 1
Portfolio item number 2
Published:
Short description of portfolio item number 2
publications
Detailed computational study of the active site of the hepatitis C viral rna polymerase to aid novel drug design Permalink
Published in Journal of Chemical Information and Modeling, 2013
This study investigates potential inhibitors of Hep C NS5B via binding free energy calculations
Recommended citation: Barakat, K. H., Law, J., Prunotto, A., Magee, W. C., Evans, D. H., Tyrrell, D. L., ... & Houghton, M. (2013). Detailed computational study of the active site of the hepatitis C viral RNA polymerase to aid novel drug design. Journal of chemical information and modeling, 53(11), 3031-3043.
Structure based modeling of small molecules binding to the TLR7 by atomistic level simulations Permalink
Published in Molecules, 2015
This study docks and evaluates potential tlr7 inhibitors
Recommended citation: Gentile, F., Deriu, M. A., Licandro, G., Prunotto, A., Danani, A., & Tuszynski, J. A. (2015). Structure based modeling of small molecules binding to the TLR7 by atomistic level simulations. Molecules, 20(5), 8316-8340.
Explaining the microtubule energy balance: contributions due to dipole moments, charges, Van Der Waals and solvation energy Permalink
Published in International Journal of Molecular Sciences, 2017
This study investigates the stability of microtubules from an energetic perspective
Recommended citation: Ayoub, A. T., Staelens, M., Prunotto, A., Deriu, M. A., Danani, A., Klobukowski, M., & Tuszynski, J. A. (2017). Explaining the microtubule energy balance: contributions due to dipole moments, charges, van der Waals and solvation energy. International journal of molecular sciences, 18(10), 2042.
Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces Permalink
Published in Journal of Virology, 2020
This study evaluates the thermostability of enteroviruses
Recommended citation: Meister, S., Prunotto, A., Dal Peraro, M., & Kohn, T. (2020). Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces. Journal of virology, 94(11), 10-1128.
Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-β-lactamase 1 Permalink
Published in ACS Infectious Diseases, 2020
This paper studies the molecular mechanism behind the antibiotic resistance of NDM-1
Recommended citation: Prunotto, A., Bahr, G., González, L. J., Vila, A. J., & Dal Peraro, M. (2020). Molecular bases of the membrane association mechanism potentiating antibiotic resistance by New Delhi metallo-β-lactamase 1. ACS infectious diseases, 6(10), 2719-2731.
Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase Permalink
Published in Chemical Science, 2020
Recognition of bacterial cell walls by bacteriophages
Recommended citation: Shen, Y., Kalograiaki, I., Prunotto, A., Dunne, M., Boulos, S., Taylor, N. M., ... & Loessner, M. J. (2021). Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase. Chemical Science, 12(2), 576-589.
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior Permalink
Published in Science Advances, 2021
This study investigates genetic variation in circadian gene expression
Recommended citation: Litovchenko, M., Meireles-Filho, A. C., Frochaux, M. V., Bevers, R. P., Prunotto, A., Anduaga, A. M., ... & Deplancke, B. (2021). Extensive tissue-specific expression variation and novel regulators underlying circadian behavior. Science advances, 7(5), eabc3781.
Specific protein-membrane interactions promote packaging of metallo-β-lactamases into outer membrane vesicles Permalink
Published in Antimicrobial agents and chemotherapy, 2021
This paper investigates the packaging of metallo-β-lactamases into membrane vesicles
Recommended citation: López, C., Prunotto, A., Bahr, G., Bonomo, R. A., González, L. J., Dal Peraro, M., & Vila, A. J. (2021). Specific protein-membrane interactions promote packaging of metallo-β-lactamases into outer membrane vesicles. Antimicrobial agents and chemotherapy, 65(10), 10-1128.
Molecular regulation and physiological role of GOLPH3-mediated Golgi retention Permalink
Published in Nature Communications, 2026
This paper elucidates the role of GOLPH3 and its molecular mechanisms
Recommended citation: Theodoropoulou, A., Nasrallah, A., Abriata, L. A., Abrami, L., Da Graça, J., Kaysudu, I., ..., Prunotto, A., ... & D’Angelo, G. (2026). Molecular regulation and physiological role of GOLPH3-mediated Golgi retention. Nature Communications, 17(1), 7426.
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown file that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
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This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Physical Biology of the Cell II
Graduate course, EPFL, School of Life Sciences, 2016
This course covered the cell and its components, including membranes, genomes, channels and receptors. Laws of physics were used to develop models to make quantitative and predictive statements. In my role I guided the students through the practical lectures, helping them with the assignments and answering to their question. I was also evaluating their final tests.
Global Issues: Health
Undergraduate course, EPFL, School of Life Sciences, 2017
The course introduced the challenges posed by biomedical innovation, infectious diseases, etc. In my role I guided the students in the completion of small 2-months projects and evaluated the written tests.
Biomolecular Structure and Mechanics
Graduate course, EPFL, School of Life Sciences, 2019
The main focus of this course is on the molecular interactions defining the structure, dynamics and function of biological systems. The principal experimental and computational techniques used in structural biology, as well as molecular modeling and design, were introduced and practiced. In my role I guided the students through the practical laboratories, and supervised them during the course of short 3-months projects. I also evaluated their final tests.