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Fig. 11 | BMC Bioinformatics

Fig. 11

From: Convert your favorite protein modeling program into a mutation predictor: “MODICT”

Fig. 11

3D models of wildtype and mutated Renin. a. Wildtype (blue) and Ren p.C20R (red) models are superimposed with the cysteine residue (green, Van der Waals) marked with arrow. Models generated with different modeling algorithms are indicated. b. Another variant in the signal sequence, Ren p.R33W (red) does not result in a change to the same extent as Ren p.C20R. The wildtype arginine residue (green, Van der Waals) is marked with arrow. Graphical representation of algorithm scores, c. Absolute values of MODICT scores obtained from pairs; negative control (left, light gray; score: 0.455), wildtype against Ren p.R33W (middle, light gray; score: 0.670) and positive control (right, light gray; score: 2.570). Algorithm scores with or without conservation (c) and weight (w) scores are also indicated (dark gray, black, see Additional file 1: Table S1). For comparison, algorithm scores generated using models from PHYRE2 is also indicated. Like black bars, these are raw MODICT scores generated without conservation and weight parameters. Sequence logo of the renin signal peptide. d. Residues 1-40 of reviewed renin sequences in UniProt database have been aligned. Note that both R33 and C20 are highly conserved, however algorithm scores significantly differ in case of I-TASSER. MODICT scores were generated taking into account the main chain (residues 67-406, UNIPROT, P00797). (W = wildtype, W R= refined wildtype)

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