i am going to model a protein (180 aa). when i blast the query sequence against PDB, it gives significant homology but coverage is >30%. I wanna to model whole protein structure, Although I have tried throgh I-TASSER but the resulted model display more than 80 % structure while other online server unable to model whole protein. Please suggest me how can i solve this problem.
first send your sequence to different servers like I-tasser. they will do loop modeling so the remaining sequences will be available and then use those server's models along with the selected templates to build the final model using Modeller.
Can you see your model file on PYMOL and can you change the preset to publication mode?
Hi Nasir,
Since you have already attempted I - Tasser and not found any results, I would urge you to first predict domains and folds of your protein using PSIPRED. You should get templates which you can use in Modeller using the Multiple Template modelling.
Once the model has been generated you can try out the CABS Flex server to simulate your protein and compare the structures (before and after simulation) for their structural conformation integrity (using Ramachandran Plot Analyses) and Geometry optimization using PROCHECK.
Hope this helps
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