id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-275258-azpg5yrh	Mead, Dylan J.T.	Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling	2019-07-26		.txt	text/plain	6333	346	53	title: Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of homology models most representative of their genera. We then present the first use of force-directed graphs to produce an intuitive visualization of sequence space, and select target RdRPs without solved structures for homology modelling. The solved structure has 10 other sequences in its proximity in the three-dimensional space, roughly Table 5 Homology modelling at intra-order, inter-family level.	./cache/cord-275258-azpg5yrh.txt	./txt/cord-275258-azpg5yrh.txt