id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-319906-s7kzp795	Zemla, Adam T	StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase	2011-06-02		.txt	text/plain	7496	303	40	When for a given reference structure a structure-based search is performed on a set of proteins from the Protein Data Bank (PDB), StralSV identifies all structurally similar fragments from that set, evaluates the calculated structure-based alignments between the query (reference) motif (designated "segment" in this work) and the detected structure fragments, and quantifies the observed sequence variability at each residue position on the query structure. (For an illustration of a "span", see additional file 1: StralSV-RdRp_Suppl_Figure 1.docx.) All residue-residue pairs that are contained within a span's alignment are used to calculate the sequence variability data at the corresponding position in the query structure. The qualified hits (structure fragments from PDB with detected local similarities to the query structure) for six selected sequence positions (positional hits) of polio RdRp (positions identified in Figure 3 ) were categorized and quantified based on SCOP (Structure Classification of Proteins database; version 1.75, June 2009 release) identifiers [32] .	./cache/cord-319906-s7kzp795.txt	./txt/cord-319906-s7kzp795.txt