Hello,
Im looking for a software (free if possible) or tool which allow me to predict a 3D structure of a transmembrane protein. The thing is I know where is the TM domain, but I would like to predict the completely 3D structure using that information.
I usually use Chimera as viewer and PSIPRED/Psyre2 as predictor, but I dont know how to force them to view/predict the 3D structure considering a particular region as "transmembrane".
Thanks!
Try I-TASSER server (http://zhanglab.ccmb.med.umich.edu/I-TASSER/). It is free and highly reliable for protein 3D structure prediction. All you need is provide the amino acid sequence (and wait: getting the prediction could take some days). Of course, I'm aware that transmembrane proteins are a special case in protein structure but if I-TASSER fails in giving you a reasonable prediction, then few (if any) alternatives remain...
You can try hhpred also. We have carried out a comparative analysis of different approaches for transmembrane complex proteins (https://www.researchgate.net/publication/281370386_Comparative_study_of_three_benchmark_protein_structure_prediction_techniques_for_the_prediction_of_epidermal_growth_factor_receptor_EGFR_family_protein_structures). Threading with its principle of fold recognition gave us better results. It was published as conference poster and now we are writing complete paper for it. Just let us know if you need any help.
Conference Paper Comparative study of three benchmark protein structure predi...
We compared both hhpred and i-tasser but hhpred gave us better results.
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