As I understand, your are working with a protein and your are looking for protein interactants, is that true? the easiest way to do this is to have your protein tagged (TAP tag could be helpful) and to do the pull down to isolate the complex followed by mass spectrometry to identify the interactants.

Hi Najeeb!!!

Do you check the similarity search of your protein sequence with the other protein sequences??

I think you can perform the BLAST and find out the similar sequences whether they are resistant proteins in rice. 

Thank you so much for your interest, here is some details about the protein, May be this will help you give me some good suggestions 

1. The protein is isolated from Magnaporthe oryzae

2. It has HR effect on tobacco leaves and could enhance the resistance to M. Oryzae while spray the protein on rice seedling 

3. I have checked some Salisilic and Jasmonic Acid pathways related genes in Rice leaves with real time PCR, that have been enhanced after treatment 

4. I have blast the protein against Rice genome, The result shows some putative proteins with query cover 48%, Identity 30%, E value 6 

5. I have checked the protein with some of the ExPASy data basis, but there is no conserved domain or motifs that help in protein interaction 

6. The predicted structure of my Protein with the help of (Phyre 2) is similar with some of the pathogenesis related proteins, with the confidence of 99% and similarity 16 - 25 %.

7. I have analysed all the proteins that come from Blast, PDB blast or Phyre2 have some specific family domains, motifs etc but my protein don't, except my proteins has some phosphorylation sites, including CK2, PKC,  and CAMP phosphorylation sites

Note: My goal is to find the binding proteins in the rice 

1. which method will be the best for me?

2. I will need the full procedure to handle it as I am new in this field  (detailed reference thesis or research paper)........

 Thanks in advance

Ok Najeeb!!!

Here you isolated protein from fungus and this will enhance the resistance to same fungus on rice seedling. Right??

I think you got better PR proteins from rice seedlings while treat the plants with the same fungus and that PR proteins may be similar with the proteins which isolated from the rice plants against SA, JA chemical induction.

One more thing, which primer you are used for real time PCR?

Go for Y2H against rice CDNA library. The best and cheapest way. as your bait is involved in PTMs, better go for Y2H. you will get accurate interaction partner. Else go for TAP affinity or make antibody against your bait and immuno-precipitate the interacted proteins. your interaction protein may be kinase or some allergens. however it may be other proteins. What Showmy told is just diverting or unwanted... if you need any help let ask me... 

Probably some useful points will be in attached article.

Article Comparative study of Surface Plasmon Resonance, electrochemi...