Pisa is a good starting point:

http://www.pdbe.org/pisa

you have do to the experiments such as isothermal titration calorimetry (ITC)

'Calculate' means measure or predict? (They are different things.) If measure, ITC for Kd and deltaH, NMR or other methods (SPR, BLI) for Kd. if predict -- good luck: binding constants/free energies are the holy grail of molecular modelling, I'd say. Also do you have the 3D structure of the complex (or even free forms)? -- you don't say.

In an isolated system?

PPN (N = network).....entropy is more relevant!!

I DID ITC , it is showing 12uM , I did NMR hsqc titration , most of the cross peaks showing intensity drop ( line broadening ).

I have free protein structures and complex structures , i want check any server can guess the binding constant near range of ITC .

I didnt find any server to guess the binding constant ! Any suggestions if anyone knows .... Please provide the link !

Try this http://structure.pitt.edu/servers/fastcontact/

I have not used ITC yet but i believe that can help you solve your problem. Sigmaplot will also be useful for Kd calculations.

The data generated by Microcal iTC200 from GE Health care uses ORIGIN software which have many models for calculating kD and delta H. For ultra-tight binding constants people also use DSC. Again ORIGIN software for Microcal DSC has built in Equation (model) to analyze data.

You 'want to check if any server can guess the binding constant near range of ITC ?'

How can you guess a thermodynamic constant ?? If you did perform the ITC experiments, obtain nice saturation curves with no background signal, it will give you a real Kd, not a guess. So it should be largely enough. Checking a result with a server to see if the result is correct, that's original !

Alex shows that " reveal a poor correlation between binding affinity and scores for all algorithms tested"

See http://haddock.science.uu.nl/services/affinity/

Currently, there are no calculation methods giving results that can reasonably match experimental results in all cases. Ernest Freire has developed some approaches based on the calculation of accessible surface areas, and has fitted the coefficients using ITC. This is probably the best approach for your case. You can read more at:

Leavitt S & Freire E (2001) Direct measurement of protein binding energetics by isothermal titration calorimetry. Current Opinion in Structural Biology 11(5):560 - 566. http://dx.doi.org/10.1016/S0959-440X(00)00248-7

Best wishes,

Rogelio

The binding constant of PPI (one-to-one) is not relevant in a many-to-many PPN where you have many proteins in a microenvironment with different concentration and affinity between them...

"The data generated by iTC200 - uses ORIGIN software which have many models for calculating kD and delta H" - yes For one to one PPI - but, Systems are not one-to-one but many-to-many “changing variables” PPN (N = network) and biological systems are dynamic open systems whereas the ITC is a closed system?...

Enthalpy is the energy of the molecules. It cannot be measured, although CHANGE in enthalpy of reactions can be measured. It's simply heat energy. Exothermic reactions have anegative enthalpy change(which means energy of the products is lower than that of the reactants). Endothermic reactions have a positive value(energy of products is higher than that of the reactants). Entropy, on the other hand, is the degree of disorder. It's the measurement of how disordered a substance is. For example, particles in a solid are regularly arranged, so they are less disordered, and have a low value of entropy.

ENTHALPHY: Is the energy content of a process (chemical, thermodynamic, mechanical, etc) that can be recovered. It is also described as useful energy.

ENTROPY: Is the energy content of a process (chemical, thermodynamic, mechanical, etc) that CAN NOT be recovered. It is also described as chaos.

It could be calculated from complex formation kinetics. In attached publication one of measurement strategies:

Article Study of antibody/antigen binding kinetics by total internal...

"calculate the binding constant and enthalpy of protein-protein interaction?" not relevant in system biology (calculate for pathological state or physiological state?)...it's related to causality...cause and effect it's always changing (in nonlinear,dynamic systems)... All the best

CE0702