Analysis of Structures and Epitopes of Surface Antigen Glycoproteins Expressed in Bradyzoites of Toxoplasma gondii

Table 3

Prediction binding site residues in the model.

Protein model	C-score^aLB	TM-score^b	RMSD^c	IDEN^d	Cov.^e	BS-score^f	Lig. name	Predicted binding site residues in the model
SAG2C	0.09	0.350	7.07	0.031	0.604	0.84	MAL	222, 223, 224, 225, 226, 227, 273, 279
SAG2D	0.11	0.435	4.90	0.043	0.668	0.75	ANP	96, 153, 155
SAG2X	0.06	0.388	5.94	0.053	0.597	0.79	NA	261, 292, 326
SAG2Y	0.07	0.412	6.36	0.057	0.687	0.77	FES	144, 145, 146, 147, 149, 150, 151, 153, 243

aC-score^LB is the confidence score of predicted binding site. C-score^LB values range between [0-1], where a higher score indicates a more reliable ligand-binding site prediction.
^bTM-score is a measure of global structural similarity between query and template protein.
^cRMSD is the RMSD between residues that are structurally aligned by TM-align.
^dIDEN is the percentage sequence identity in the structurally aligned region.
^eCov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
^fBS-score is a measure of local similarity (sequence and structure) between template binding site and predicted binding site in the query structure.