Three adenosine-binding residues were identified based on human cryptochrome DASH (chain X; PDB ID 2IJG) [ 31, 32], six phosphate-binding residues were identified based on photolyase-like domain of cryptochrome 1 (chain A; PDB ID 1U3C) [ 33], eleven flavin-binding residues were identified based on photolyase (chain A; PDB ID 1IQR) [ 34], and four were identified based on other protein templates.
Nine nicotinamide-binding residues were identified based on aldehyde dehydrogenase (chain A; PDB ID 3B4W), three phosphate-binding and eight adenosine-binding residues were identified based on 1-pyrroline-5-carboxylate dehydrogenase (chain A; PDB ID 2EHU), and three were identified based on other protein templates.
Under these same conditions, FAD-binding residues were identified with an accuracy of 94.33%, a sensitivity of 64.13%, a specificity of 96.27%, and an MCC of 0.55 (Table 2).
First, a multiple sequence alignment generated by Buzko and Shokat [1] was adopted and binding site residues were identified.
Hydrogen bonding interactions between ligands and binding site residues were identified using the hydrogen bond monitor function in ViewerLite (www.accelrys.com).
From a comparison of the crystal structures of RAD51 and RadA in the immediate vicinity of the FXXA binding pocket, six key residues were identified that differed between the two proteins.
The active ATP binding sites consisting of 15 amino acid residues were identified and the total energy (Etotal) which showed the affinity between the inhibitor molecules and the receptor (Van der Waals and electrostatic interactions).
Several key residues were identified to be responsible for the binding of indole and benzphetamine with CYP2W1.
Proximity of putative binding site residues with respect to variant amino acid residues was identified by using a 5 Å sphere radius from the binding site amino acid residues under PyMol.
When the QacR sequence was analyzed using BindN, the false positive rate was very high (58 false positive predictions for the 166 non-binding residues) although all the 12 DNA-binding residues were correctly identified.
