What do you mean by characterising the est?

I mean developing an insilico protien model for the est , as its function is not defined and carry out the protien-protein interaction study by docking with other protiens.

Your question is not clear. Whats the percentage of homology with your protein? If it matches, it should be the part of your protein encoding gene/genefamily. Anyway, If you have the EST sequence, do the BLASTx against PDB at NCBI. If you find significant match in any structure in PDB, you can use that as a template to model your protein by homology modeling in Swiss-Model server or Modeller program. Then, you can use protein-protein docking study using several other programs. But you must do it with caution. Because, most of the cases, modeled structure doesn't produce accurate result. And to my knowledge, there is no such docking program that can predict protein-protein interaction accurately.

Thank you very much Mr.Amin for the answer, during the work even i also find that docking program did not predict protein-protein interaction accurately. There is one more doubt i want to clear. Out of the two proteins which i want to use for docking i got EST of only one protein at NCBI, for that i will follow the approach you mention in your reply, for other protein i derived its amino acid sequence by finding ORF in its nucleotide sequence. Is this a valid approach.

If you are to model the protein (amino acid seq.), why are you talking about EST (nucleotide seq.)? I guess your EST is a short fragment and If it comes from the UTR of gene, you'll not get any match with amino acid sequence of a protein. Is it a human sequence or other species? How did you get that EST, from database or from your own experiment? Why don't you map the EST with its genome and get the information about the protein and then, deal with amino acid sequence of that particular protein? Whats your ultimate goal?

Thank you for your candid reply Mr.Amin. I am working on pathogens of citrus, Phytophthora is one of the major citrus plant destroyer. I want to study interaction of two proteins (one from citrus and one from Phytophthora) involved in pathogenesis. now i got an EST (from database) from citrus which is involved in pathogenesis. but for Phytophthora (species of my interest) i didn't find any notable EST, but i know the name of the protein from other Phytophthora species (not of my interest) so i searched NCBI for the homologous sequence within my Phytophthora species of interest and i got one. but genome of Phytophthora species in which i am interested is not still sequenced that's why i derived a amino acid sequence from that nucleotide sequence. now i want to develop the protein structure from this sequence and carry out docking study for two proteins (one from citrus and one from Phytophthora) and find out the interactions between them. In that case what should be my approach.

I don't have experience of working with the genome of plant/plant pathogen. You can try according to my previous post.

K. once again thank you.

HEX tool is best for protein-protein docking can I involve in you topic its quite interesting I have one idea on your topic first study the protein protein interaction and find chemical inhibitor to inhibit interaction. Study the area of amino acids involved in protein-protein interaction carefully observe both protein amino acids structure and design a chemical inhibitor it should not harm for other organic compounds in citrus plant. If you are interested to involve me in your topic I will help you out in modelling.

In my opinon one thing that you should try and do is a 5 prime and 3 prime race experiment. now that you have got your est you can design primers and see what you get. I know in mammalian cells this is often what researchers do and so i persume you could do the same in plant cells. Once you have this data it will be more useful to you in obtaining the proper/full protein structure as with an est you most likely only have a small part of the protein however its not possible to rule out that maybe the est you have also may encode the full protein.

Thank you Dr, Durcan for sharing your opinion.