Fig. 5
From: In silico optimization of RNA–protein interactions for CRISPR-Cas13-based antimicrobials
Best crRNA candidates for Cas13a protein from in silico docking experiments. The 3-D visualization shows the spatial coordinates of each crRNA candidate model (only 10 best models were considered) after in silico docking with the corresponding Cas13 protein. Each pink dot represents the centre of mass calculated from all atoms of the macromolecular structure model for each crRNA candidate. The GT crRNA is marked as a black dot, and its closest crRNA candidates in terms of Euclidian distance are highlighted as blue dots. The multiple sequence alignment compares the RNA sequences of the GT crRNA with those of the best crRNA candidates. The different shades of blue show the percentage identity, with the identity threshold set to 50%, highlighting variations in the RNA sequences. The 3-D structure shows an example of docking between the receptor (Cas protein) and the ligand (crRNA). The Cas proteins are in grey, the GT crRNA is coloured in magenta, and the best crRNA candidate model is highlighted in green with its identifier given above (GenomeID_CRISPRarray_CRISPRrepeat_modelnumber)