BioMed Research International / 2013 / Article / Tab 3

Research Article

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 TM-scorebRMSDcIDENdCov.eBS-scorefLig. namePredicted binding site residues in the model

SAG2C0.090.3507.070.0310.6040.84MAL222, 223, 224, 225, 226, 227, 273, 279
SAG2D0.110.4354.900.0430.6680.75ANP96, 153, 155
SAG2X0.060.3885.940.0530.5970.79NA261, 292, 326
SAG2Y0.070.4126.360.0570.6870.77FES144, 145, 146, 147, 149, 150, 151, 153, 243

C-scoreLB is the confidence score of predicted binding site. C-scoreLB values range between , 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.