id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-296997-ba7f2mf3	Sikora, Mateusz	Map of SARS-CoV-2 spike epitopes not shielded by glycans	2020-07-03		.txt	text/plain	5818	371	55	To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. Our simulation system contained four membrane-embedded SARS-CoV-2 S proteins assembled from resolved structures where available and models for the missing parts (SI Appendix, Fig. S5 ). In the ray analysis, we illuminated the protein model by diffuse light; in the Fab docking analysis, we performed rigid body Monte Carlo simulations of S and the SARS-CoV-2 antibody CR3022 Fab to determine the steric accessibility to an antibody Fab. To account for protein and glycan mobility, we performed both analyses individually for 4 × 193 snapshots taken at 10 ns time intervals from the 1.93 µs MD simulation with four glycosylated S proteins.	./cache/cord-296997-ba7f2mf3.txt	./txt/cord-296997-ba7f2mf3.txt