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Fig. 1 | BMC Systems Biology

Fig. 1

From: Network topology of NaV1.7 mutations in sodium channel-related painful disorders

Fig. 1

NaV1.7 computational protocol overview. A NaV1.7 WT homology modelling of based on the bacterial NavAb sodium channel template. B Energy minimization and structure refinement of the protein structure with YAMBER force field and FG-MD server. C In-silico mutagenesis for pathogenetic and control group (nABN/hSNPs) mutations. D Transforming NaV1.7 structure into residue interaction graphs. The construction of inter-residue network was based on interatomic bonds (hydrophobic, hydrogen bonds, salt-bridges, cation-π and π-π stacking interactions) using the commands “ListIntAtom” and “ListIntBo” via YASARA software. The de novo network construction for each mutant and WT models is achieved considering the predicted binary interatomic bonds. E-F. Network centrality calculation and their relative variation between mutant and WT (Δ value  = mutant value -WT value )

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