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PreDDICTA
Here you can Predict DNA-Drug Interaction strength by Computing ΔTm and Affinity of binding.

PreDDICTA employs an all atom energy based function for predicting the binding affinity of a DNA oligomer with a non-covalently bound drug.   Click here to know more about DNA Drug interaction

The function has been validated [1] via correlation with experimental data on change in melting temperature of the DNA oligomer upon drug binding, ΔTm and binding free energy, ΔG°bind for DNA Drug complexes.

PreDDICTA can be used for three purposes :

Complex of DNA oligomer with minor groove binder Netropsin (PDB ID: 121D)
Predict ΔTm and Δ G°bind from 3-D structure
Select Option                          Approximate                                                            Help
                         Accurate      Formal Drug Charge
Input
                         Input PDB file :   [Sample Files]

                         E-mail address:


Output

Predict Binding Affinity from ΔTm
If you have determined the ΔTm for a DNA-drug complex and wish to predict the binding affinity in terms of binding free energy, then do use this utility.
Input ΔTm  Kelvin  

Predicted Binding Free Energy  kcal/mol

Predict ΔTm from Binding free energy
If you have the binding free energy value for a DNA drug complex, then you can predict the change in melting temperature of oligomer upon binding from this utility.
Input Binding Free Energy kcal/mol  

Predicted ΔTm  Kelvin

References:
[1] "A Computational Tool for Predicting DNA-Drug Binding Affinity and .Tm" Saher Afshan Shaikh and B.Jayaram, 2006,Manuscript submitted.

[2] "A second generation force field for the simulation of proteins, nucleic acids, and organic molecules." W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell and P.A. Kollman. J. Am. Chem. Soc 1995, 117, 5179.

[3] "Development and testing of a general Amber force field." J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman & D.A. Case. J. Comput. Chem. 2004, 25, 1157.

[4] "Iterative Partial Equalization of Orbital Electronegativity - A Rapid Access to Atomic Charges., J. Gasteiger and M. Marsili. Tetrahedron 1980 36, 3219.

[5] "Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: I. Method." A. Jakalian, B.L. Bush, D.B. Jack and C.I. Bayly. J. Comput. Chem. 2000, 21, 132.