I just start to use Firedock trying to establish whether a complex could be formed between a very large protein for which a crystal structure is available and a smaller protein fragment for which I determined an NMR structure. From my NMR data I know that only a fragment of roughly 25 residues is well ordered, but for a correct docking I suppose that I also should integrate residues from the surrounding, flexible part. Now I saw that in the advanced options that one could define "flexible residues" - I saw from the Nucl. Acids. Res. paper that flexible means that sidechains are not fixed but flexible - but what does this flexible mean compared to sidechains that have neither been declared "fixed" nor "flexible" ? And is there a way to introduce backbone mobility ? I suppose that the problem then gets too complex ....

I would also like to know how protons are handled ? Does the programs (PatchDock and FireDock) introduce protons to crystal structures before docking ? Or do I have to remove protons from my NMR structure to obtain something meaningful ? Or do I have to introduce protons myself before submitting a crystal structure to the docking program ? What about the influence of protons on the electrostatics calculation ?

Unfortunately the email addresses provided on the program's homepage do not seem to function anymore.

Thanks for your comments

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