I have a trimeric protein which have a lots of missing residues. that why i decided to build homology modelling. but after successfully modelling each chain contains maximum loop like structure which is not stabilized. so can one help me to make it helical like structure. here i attached one chain of the protein.
Questions:
1. How many residues are missing? Are the missing residues in loop regions or regions with secondary structure such as beta strands or alpha helices? You might be able to build/repair loops rather than doing complete homology modeling.
2. Which software are you using for homology modeling?
here i attach the picture where the reports reveal the gap present in the structure. but i dont know the actual structure is loop or helices or beta sheet?
i am utilizing the modeller for generating model structure.
But i dont know how solve the gap region
If you do not mind sharing, if the starting structure is in the PDB, could you send the PDB ID number? Thanks.
actually it is a little bit confidential..and the structures shares a maximum helical structures. here I attach a snapshot for structure prediction.
can you help me out?
Sourav Pal,
I regret I would not be able to assist you with only the sequence information you have provided.
RJR
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