PDA-Pred Protein-DNA complex Binding Affinity Prediction

PDA-Pred

This server predicts protein-DNA binding affinity using structure-based features and classes based on structure, function and percentage of binding site of protein. Generally, contact potenitals, accessible surface area, interactions between various atoms and their energy contributions, base step parameters of the DNA, secondary strucutres and residue depth of protein are important to understand the binding affinity. PDA-Pred shows a correlation of 0.86 and a mean absolute error(MAE) of 0.76 in Self-consistency, correlation of 0.78 and a MAE of 0.98 kcal/mol in jack-knife test. Users can download source code from: https://github.com/Harinikannan98/PDA-PreD

Please click here to start prediction.

ZIF268 Zinc finger-DNA complex (PDB:1AAY)

Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA (PDB:1GLU)

Crystal structure of human interleukin 6 in complex with a nucleotide aptamer (PDB:4NI7)

Crystal structure of Sulfolobus Cren7-dsDNA(GTGATCAC) complex (PDB:4R56)

Crystal structure of pre-specific restriction endonuclease BsaWI-DNA complex (PDB:4ZSF)

Crystal structure of horse TLR9 in complex with agonistic DNA1668_12mer (PDB:3WPC)