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Fig. 1 | BMC Bioinformatics

Fig. 1

From: Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Fig. 1

Scheme of the input data and screenshot of PsychoProt when displaying the Core Results (top half) and when mapping results on structure (bottom half). In the gray window on top, the list of all fits that satisfy the p-value cutoff is on the left, the list with only the best fits for each residue is in the center, and a plot of the currently selected fit is shown on the right. The ribbon of buttons leads to further outputs as exemplified in Additional file 1: Figures S1 and S2. The gray window at the bottom opens when the user clicks “Map on 3D structure” in the ribbon of buttons. Here the user choses first a PDB ID (in this case 1XPB [65]) and the chain corresponding to the protein of interest (top left, labelled “Start here”) and clicks “Load”. The protein backbone is automatically shown as cartoons, here colored according to the tolerance to substitution (k*) which ranges from blue (low tolerance) to white to red (high tolerance). All residues whose best fit was against hydrophobicity with a negative trend (i.e. favoring hydrophilic amino acids) are shown as sticks (of which Glu28 is also rendered as spheres because it was clicked in the list). Three active site residues are also rendered as green spheres. This collage corresponds to the analysis of amino acid variability in a structure-consistent alignment built from TEM-1’s sequence, and is available as a sample dataset in the website

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