Hello I hope you are all doing well.:)
Several transmembrane Pannexin1 3-D coordinate files have been submitted to the PDB, however, I believe all are missing coordinates in some of the Pannexin1 coils and or loops, accordingly I believe it would be best to just ab initio model these portions and then cut and paste these coordinates back into the proper PDB coordinate file before GROMACS simulating would you agree that this would be the best methodology in this case?
Thanks:) Joel
Hello, yes, it is valid, since a common problem in PDBs is the lack of portions corresponding to loops in the protein, I would recommend: 1) make a complete model using I-TASSER, indicating in the constraints that it uses the structure of the protein PDB as a base 2) You will model those loops separately, join them and minimize the area (Maestro, it is useful in those cases).
If you choose the second option, try to leave about 5-10 extra residues so that it is easy to align with the reference structure and you can join them
I hope this answer is useful
Best regards
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