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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), where I am now an Associate Professor. My research focus then moved to the computational study of enzymatic and organic reaction mechanisms using quantum chemistry and molecular dynamics methods.
I have been an Academic Editor for PeerJ since September 2015, and Section Editor for its "Biochemistry, Biophysics and Molecular Biology" section since its creation in February 2018.
Biochemistry Bioinformatics Bioinorganic Chemistry Biomolecules Bioorganic Chemistry Biophysical Chemistry Biophysics Biotechnology Catalysis Microbiology Molecular Biology Physical Organic Chemistry Theoretical & Computational Chemistry
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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....