I have a question on the data in Bsites_model1.dat generated by COFACTOR. For the binding residues listed at the end of each row in Bsites_model1.dat, are these the binding residues at the query sequence or at its similar structure found in PDB (represented by PDB id and shown in the third column)?
Below is a sample entry in Bsites_model1.dat:
1 0.976 2mghA 0.9848 0.6300 0.9870 1.0000 HEM BS01 1.9649 0.9939 0.9709 1.0000 0.5084 0.9444 0.9375:40,43,44,65,68,69,72,90,93,94,98,100,104,105,108,139