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Pedro J. Silva
Summary
My PhD research centered on the characterization of enzymes involved in hydrogen metabolism in the hyperthermophile Pyrococcus furiosus. After completing my PhD, I became an Assistant Professor at Universidade Fernando Pessoa (Porto, Portugal). My research focus then moved to the computational study of enzymatic and organic reaction mechanisms using quantum chemistry methods. I have been an Academic Editor for PeerJ since September 2015.
Biochemistry Biophysics Cell Biology Metabolic Sciences Microbiology Molecular Biology Parasitology Pharmacology Toxicology Virology
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Articles published in PeerJ
Refining the reaction mechanism of O2 towards its co-substrate in cofactor-free dioxygenases
Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?
Mechanistic pathways of mercury removal from the organomercurial lyase active site
Preprints
Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases
Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?
Mechanistic pathways of mercury removal from the organomercurial lyase active site
Academic Editor on
Effects of arginine vasopressin on the urine proteome in rats
Tartrazine induces structural and functional aberrations and genotoxic effects in vivo
Modafinil decreases anxiety-like behaviour in zebrafish
Effects of rhodomyrtone on Gram-positive bacterial tubulin homologue FtsZ
Prediction of pKa values using the PM6 semiempirical method
An explicit-solvent conformation search method using open software
Exploring the chemical space of influenza neuraminidase inhibitors
Adaptation prevents the extinction of Chlamydomonas reinhardtii under toxic beryllium
Computational inference of H3K4me3 and H3K27ac domain length
Proteome-wide prediction of targets for aspirin: new insight into the molecular mechanism of aspirin
Provided feedback on
Towards a barrier height benchmark set for biologically relevant systems
This is a nice paper, even though the results are frustrating for those who expect that semi-empirical methods will soon become a useful alternative to DFT in real-life application...
Minor points: p. 19 "Procerain, a stable cysteine protease […] was found to have a molecular mass of 28.8KDa and an isoelectric point of 9.32." The original paper (Dubey, VK a...
Other minor points: Figs 25-35: The xx axis are labeled “enzyme concentration” instead of urea /CaCl2, NaCl, etc… concentration. Are those concentrations final concentrations or (...
Other Major points: The data on figs 9-18 are extensively described verbally, which is redundant as proper graphs tell the story much more effectively. An attempt to discuss,...
line 120: " the name of either the region, or various localities within the region (e.g., “Ireland” and “England” for the Western Atlantic)." Should it not be Eastern Atlantic?...