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Pedro J Silva
Summary
I was originally raised as en experimental Biochemist. My PhD research (1996-2000) centered on the biochemical characterization of the soluble hydrogenase of the hyperthermophile Pyrococcus furiosus. Eventually, the research focus broadened to include other metalloproteins from P. furiosus, which were characterized by biochemical, electrochemical and spectroscopic methods (electron paramagnetic resonance, UV-Vis spectroscopy, cofactor analysis, bioinformatics, enzymology, etc.).
In 2001, 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 and molecular dynamics methods. I left that position in August 2023 to become Staff Editor at PeerJ.
I had been an Academic Editor for PeerJ since September 2015, and Section Editor for its "Biochemistry, Biophysics and Molecular Biology" section from its creation in February 2018, to the end of May 2023.
Biochemistry Biophysical Chemistry Cell Biology Microbiology Molecular Biology Physical Organic Chemistry Synthetic Biology Theoretical & Computational Chemistry
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Academic Editor on
Signed reviews submitted for articles published in PeerJ Note that some articles may not have the review itself made public unless authors have made them open as well.
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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?...
I found out that the basis set used is insufficient for proper optimizations. I have now redone the whole computations with (aug)-pcseg-1 and computed single points with DSD-BLYP....