Pedro Alexandrino Fernandes

Computational Biochemistry, University of Porto

Pedro Alexandrino Fernandes


I got a degree in chemistry at the University of Porto, Portugal, in 1993. After teaching chemistry in high school for three years, I started my Ph.D. studies (1997) under the supervision of Prof. José Gomes. The subject of my work has been simulations of liquid|liquid Interfaces and ion transfer across them. Upon finishing my Ph.D. (2000), I became an Assistant Professor at the Chemistry Department of the Faculty of Sciences of Porto, Portugal. I am now a Full Professor of the same Faculty.

I teach courses for the degrees and MSc in Chemistry, Biochemistry, and Bioinformatics, mainly in quantum chemistry, computational biochemistry, and drug discovery.


My research began with a brief passage through path integral Monte Carlo simulations. Afterward, I spent a few (Ph.D.) years dedicated to classical molecular dynamics simulations of liquid|liquid interfaces and ion transfer across liquid phases. Finally, my interests shifted toward biological systems after finishing my Ph.D.
I now research enzymes' reaction mechanisms using QM/MM methods. In recent years, my research has also focused on the relationship between enzyme flexibility, reaction rate, and computational enzyme evolution through rational enzyme engineering.
Other research areas I work in include the energetics and dynamics of proteins; diffusion of small druglike molecules across biomembranes;  molecular dynamics free energy calculations in proteins; molecular docking; and drug discovery.
My recent projects apply the abovementioned methods to manage several societal problems. Specifically, I am working on understanding snake venom chemistry and its molecular mechanisms of pathophysiology. In addition, I am developing new antidotes against snakebite envenoming, the most problematic Neglected Tropical Disease, and turning snake venom components into new therapeutic drugs.
I am also working on new methods for plastic bio-recycling using enzymatic methods. I work to discover new plastic-degrading enzymes and the engineering of know enzymes to make them more suitable for application at an industrial scale.



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