id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-255293-8necodtw	Phakthanakanok, Krongsakda	A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism	2009-01-30		.txt	text/plain	3958	222	63	The purpose of this research is to investigate the binding mode between the SARS CoVMpro and two octapeptides, especially in the region of the S3 subsite, through a molecular docking and molecular dynamics (MD) simulation approach. In order to perform molecular dynamics simulations, three structures of the SARS CoVMpro complexed with the octapeptides obtained from the docking, were prepared. However, one atom of the Na+ was also added in each system of the enzyme-substrate complexed of the octapeptide P3Lys and P3Arg due to it neutralized the amino acid, Lys and Arg. In the simulation, each time step was set to 2 fs and the simulation of the whole system performed for 2,000 ps (2 ns). The structure of the enzyme-substrate complex (SARS CoVMpro-octapeptide) obtained from molecular docking was then subjected to MD simulation.	./cache/cord-255293-8necodtw.txt	./txt/cord-255293-8necodtw.txt