Pedro Alexandrino Fernandes

Computational Biochemistry, University of Porto

Pedro Alexandrino Fernandes


I have got a degree in chemistry at the University of Porto, Portugal, in 1993. After teaching chemistry in the high school for three years, I have started my PhD studies (1997), under the supervision of Prof. José Gomes. The subject of my work has been aimulations of liquid|liquid Interfaces and ion transfer across them. Upon finishing the PhD (2000) I become an Assistant Professor at the Chemistry Department of the Faculty of Sciences of Porto, Portugal, and later (2009) an associate Professor of the same Faculty. I teach courses for the degrees and MSc of Chemistry and of Biochemistry, mostly in the field of quantum chemistry, computational biochemistry and drug discovery.


My research began with a brief passage through path integral Monte Carlo simulations. Afterwards I have spent a few (PhD) years dedicated to classical molecular dynamics simulations of liquid|liquid interfaces and ion transfer across liquid phases. My interests shifted towards biological systems after finishing my PhD, and I began studying the reaction mechanism of enzymes, first using density functional theory and small enzyme models, and afterwards using QM/MM methods and large enzyme models. A particular focus of my research in the recent years has been the relationship between enzyme flexibility and reaction rate. My research areas now encompass the energetics and dynamics of proteins, diffusion of small druglike molecules across biomembranes, molecular dynamics free energy calculations, computational mutagenesis (mostly alanine scanning mutagenesis), docking algorithms (with emphasis on protein:protein docking) and drug discovery.


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