I had used different protein-protein tools like Hex, patch dock, zdock, prodock etc., all are showing similar kind of +ve energies, but when I cut model into two different chains they are showing very good docking energies with my ligand protein?
The 3D conformation of your modelled protein structure might not be appropriate for the interaction. Please search for the appropriate ligand binding cavity in your protein using online tools such as CastP. The corresponding amino acid residues can be given as input while defining the locus of interaction. You can use HADDOCK program for docking.
Main problem is the conformation of the modelled protein. When you are breaking your protein model into two different chains, the binding residues are exposed, which might be in burried location in the full model. So goinf for blind docking will not be of much use. If you have any prior information of the binding residues, it will be very useful. If not, then use the cavity analysis tools and select the most appropriate cavity for binding.
cheers
Ambuj
Total residue number is 2000, it means your structure is some kind of multimer. first of all you have to check for functional structure of your protein that mean, functionally your protein is monomer , di or trimer so on by help of literature.. if your protein is functional in dimer/tri then no need of doing docking for full multimer structure.before docking you have to search for good cavity by help of Castp or Q-site finder then perform docking and simulate the structure.
what i feel is that this 2000 residue form club structure where entry of ligand is difficult or may be your protein molecule is in inactive state.
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