PubMed offers a connection to the UNIX terminal through the ncbi-entrez-direct package distributed through the apt repository. Documentation can be found here. Installation is as follows.
sudo apt install ncbi-entrez-direct
Then I was thinking of searching COVID-19 articles for new targets and then looking for the word
Spike inside that through the
grep function of UNIX and then piping it to a file. Spike is a coronavirus receptor which is one of the main targets for COVID-19 (Reference). I also wanted to print 2 lines above and 2 lines below for understanding the context.
esearch -db pubmed -query "COVID-19 AND target" | efetch -format abstract | egrep -i '^(Spike|"spike protein"|spike)' -A 2 -B 2 >> "Store1.txt"
proprotein convertase furin, reducing its dependence on target cell proteases for entry. The high hACE2 binding affinity of the RBD, furin preactivation of the spike, and hidden RBD in the spike potentially allow SARS-CoV-2 to maintain efficient cell entry while evading immune surveillance. These features may contribute to the wide spread of the virus. Successful intervention strategies -- The pandemic coronavirus SARS-CoV-2 threatens public health worldwide. The viral spike protein mediates SARS-CoV-2 entry into host cells and harbors a S1/S2 cleavage site containing multiple arginine residues (multibasic) not found in closely related animal coronaviruses. However, the role of this multibasic -- immunity responses (decoy cellular vaccination) in the prevention of COVID-19 disease is currently being explored. Our approach entails utilizing SARS-CoV-2 Spike antigen-expressing, non-replicating cells as carriers and presenters of immunogenic antigens, so called "I-cells". By using irradiated cells as presenting vehicles of SARS-CoV-2 viral antigens(s) in a cellular context, these -- mechanism across the CoV family make it a valuable target to elucidate and develop pan-CoV therapeutics. In this article, we review the role of the CoV spike protein in mediating fusion of the viral and host cell membranes, summarizing the results of research on SARS-CoV, MERS-CoV, and recent peer-reviewed studies of SARS-CoV-2, and suggest that the fusion mechanism be -- The outbreak of a novel coronavirus (2019-nCoV) represents a pandemic threat that has been declared a public health emergency of international concern. The CoV spike (S) glycoprotein is a key target for vaccines, therapeutic antibodies, and diagnostics. To facilitate medical countermeasure development, we determined a 3.5-angstrom-resolution cryo-electron microscopy structure of the 2019-nCoV S
- Power of awk and sed can be brought in
- Faster than even PubMed search
- To the point results can be obtained
- Ability to utilize shell scripting
crontabfor routine checking for any new results without the manual requirement to have a look into PubMed.
pdfgrep can be brought into action to read many pdfs at a time and many more. For eg
pdfgrep "Spike" *can be used for searching for the "spike" (protein) word in all the PDF's present in the directory.
Let's show our power of Ubuntu!!!