I am a beginner to rosetta, and I was wondering if there is a way to truncate/ get rid of a specific part of a sequence and create a stable protein? I have the PDB of the protein and the specific parts of the sequence I need to truncate. It is to get rid of loops at the terminus. Do I just input a sequence to rosetta with the unwanted parts deleted and have it model the protein ?
Sequence :
G-SPELREKHRALAEQVYATGQEMLELREKHRALAEQVYATGQEMLKN-TSN
SPELREKHRALAEQVYATGQEMLELREKHRALAEQVYATGQEMLKN-GVSP
SPELREKHRALAEQVYATGQEMLELREKHRALAEQVYATGQEMLKN-TSN
SPELREKHRALAEQVYATGQEMLELREKHRALAEQVYATGQEMLKN
Parts bolded are those I want to remove. In the photo attached is the circled area of the protein i'd like to remove.
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 Protein.jpeg | 44.24 KB |
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Post Situation:
Honestly, to create an initial structure for further use, I would just put the sequence without the loops into AlphaFoldor RosettaFold and predict the structure (with MSA if natural, single sequence if designed). Then, relax it with Rosetta if you want to use it for further modeling/docking/etc.
Thanks ! I just ran it through alphafold and came back with very high confidence scores all around without the loops. Unfortunately the hemes inside where not processed, but i think thats due to the sequence not having the heme mentioned. I'll look around to see if there is any way to incorporate the hemes inside using rosetta.