Hi,

I would appreciate in getting support to solve a Protein Homology problem.

I have no practical  experience with this, (except some practice with 'happy end' examples in tutorials), so do not spare words with important details.

Data available:
1-The crystall complex, Protein+Ligand(=BY106830) is with 3.0 Angstrom resolution (1R20.pdb)
-1R20.pdb: It is related to the moth Heliothis virescens heterodimer EcR-USP (Ecdyson Receptor with ultraspiracle, the homolog of retinoid-X receptor). 

2-Literature provides amino acid sequences of SeEcR (army worm Spodoptera exigua ecdysone Receptor)
Sequences available:  SeEcR (A), SeHR3 (B), and  SeFTZ-F1 (C) PCR fragments. I will have to copy them manually as the codes of GeneBank does not retrive anything when using literature informed codes (EU496824, EU496825,EU496826).

One final important comment. From literature I learned that a very high homology exists amongst
amino acid sequences of other moth species(Lepidoptera): 80% to 96%. So I 'believe' that something in this % range should occur for SeEcR-USP protein complex.

SO What:

3- (a) I need to build the SeEcR protein, but  preserving the USP part of 1R20. In other words,at the end I will obtain and SeEcR-USP heterodimer;
   (b) OPTIMIZE it with some MM or MMFF forcefield ( I suppose that this is done before homology is carried out, or not?);
   (b) make the homology study between 1R20.pdb and the SeEcR-USP;  
   (d) get RMSD amongst binding sites (if possible). Any script/software recommendation?

4- Start docking procedures with BY106830 analogues in the SeEcR-protein = Main Target of my research!  

I need help only to item (3).

Core question: What are the steps to be followed in order to correctly use the available data and obtain reliable theoretical results using  DS 3.0.

Thank you
Regards
Bruno