PDA-Pred

Protein-DNA complex Binding Affinity Prediction

What is PDA-Pred?

PDA-Pred is a webserver to calculate the binding free energy (ΔG in kcal/mol) of protein-DNA complexes. It uses structure-based features and regression model to predict ΔG in kcal/mol.

What is the advantage of using PDA-Pred?

PDA-Pred uses structure-based features to predict the change in binding affinity (ΔG value, kcal/mol) in protein-DNA complexes.

Note: It does require structural data as input. Thus, it can be used for protein-DNA complexes for which structure is available.

Run the prediction mode locally?

Users can download source code from: https://github.com/Harinikannan98/PDA-PreD Local instaltion would be recommended for huge complex, that might require, huge computation and cases where the output is not generaed due to error in external softwares, Local installation could be a better solution.

Why is my input is not being accepted by the server?

There are a number of reasons why our server may not accept a given input. Please ensure that:

The structure contains DNA chains.
The mentioned PDB ID and chain identifier is correct and availble in the PDB database.
The user uploaded PDB file does not match with pdb format.

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