Kindly suggest your views on the topic. Please provide references wherever possible.
Yes. For example I would like to model Drosophila OR 42a UniProtKB - Q9V9I2
>sp|Q9V9I2|OR42A_DROME Odorant receptor 42a OS=Drosophila melanogaster GN=Or42a PE=2 SV=3
MDLRRWFPTLYTQSKDSPVRSRDATLYLLRCVFLMGVRKPPAKFFVAYVLWSFALNFCST
FYQPIGFLTGYISHLSEFSPGEFLTSLQVAFNAWSCSTKVLIVWALVKRFDEANNLLDEM
DRRITDPGERLQIHRAVSLSNRIFFFFMAVYMVYATNTFLSAIFIGRPPYQNYYPFLDWR
SSTLHLALQAGLEYFAMAGACFQDVCVDCYPVNFVLVLRAHMSIFAERLRRLGTYPYESQ
EQKYERLVQCIQDHKVILRFVDCLRPVISGTIFVQFLVVGLVLGFTLINIVLFANLGSAI
AALSFMAAVLLETTPFCILCNYLTEDCYKLADALFQSNWIDEEKRYQKTLMYFLQKLQQP
ITFMAMNVFPISVGTNISVTKFSFSVFTLVKQMNISEKLAKSEMEE
Ok then the best way is to make a homology model using at least 2 softwares.
The best one available are iTasser and Swiss Model. Given that it is drosophila, many templates will be available. If you need help with the interpretation of results , feel free to contact
good luck !
Thank you for the suggestion. Although templates with good sequence identity are not available for insect olfactory receptors. Also iTasser predicts a structure which does not support experimental observations. I will give a try to Swiss Model.
Swiss model relies even more on templates.
Can you elaborate on the 'experimental observations' and as to why it would not be coherent with the prediction model by iTasser ?
The experimentalists have proven that the insect olfactory receptors possess 7 transmembrane helices with big loops. iTasser predicts 9 to 12 helices with small loops. So it does not seem to be coherent.
Dear Snehal,
I would like to suggest you RaptorX (http://raptorx.uchicago.edu/StructurePrediction/predict/) structure modeling, or Modller (loop modeling and optimization). MODWEB server.
Using Multi-template and selection of suitable template was best in Raptor X.
Hope it is useful.
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