In silico optimization of RNA–protein interactions for CRISPR-Cas13-based antimicrobials

Biology Direct

Table 1 Superimposition performance of the predicted crRNA structure with the ground truth crRNA structure

RNA 3-D structure prediction program	RNA 2-D structure prediction program	Mean RMSD value (Å)	Standard deviation of RMSD values (Å)
RNAComposer	CentroidFold	14.5751	3.4605
	ContextFold	15.0601	6.7700
	CONTRAfold	13.0886	3.9715
	IPknot	15.5927	4.3685
	MXfold2	13.3285	3.3359
	RNAfold	13.8130	4.0411
	RNAshapes	13.4816	4.3896
	RNAstructure	13.5431	4.2974
Rosetta	CentroidFold	11.4316	3.9693
	ContextFold	13.2483	4.9258
	CONTRAfold	11.8012	4.3517
	IPknot	9.9731	3.4309
	MXfold2	11.1416	3.8934
	RNAfold	11.9661	4.6712
	RNAshapes	11.8083	3.5449
	RNAstructure	12.8113	5.3425

Performance of the RNA 2-D structure prediction programs in combination with RNAComposer or Rosetta when superimposed to the GT 3-D structure of the experimentally validated crRNAs. The mean and the standard deviation of the root-mean-square deviation (RMSD) values were calculated from three replicate runs of PyMOL align across all the predicted structures

ISSN: 1745-6150