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Feature requests / Re: Mutate_Bases: Option to mutate all residues of the same type to another
« on: December 29, 2018, 02:31:56 am »
Hi Xiang-Jun,
First of all, thanks a lot for your earnest response. With regards to your first query, I am not sure if there are any available software tools for sugar mutations. However, please let me know if you find/are aware of any such tools for sugar mutations. It would be of great help to me.
' Cannot you do it manually? '- I can do it manually but i will have to worry about the dihedral angles and bond length in the case of the mutated sugars and it might be inconsistent with the conformation that i have taken from the fiber model from web x3dna 2.0. So, O2'-C2'-C3'-C4' dihedral is the main cause of my concern.
' How do you consider the sugar conformations (C3'-endo vs C2'-endo) after adding O2' ?'- Ideally, I would like to have the sugar conformations unchanged for the modified bases after addition of O2', if there are no steric clashes. Then, I want to see what changes come up over time to these forcibly retained bases, through MD simulations.
' Do you have a concrete example of such mutations? '- Yes, there are many examples of such mutations in literature. Please go through either of these links to have a rough idea of what I am trying to study:
1- https://onlinelibrary.wiley.com/doi/full/10.1002/cbic.201600385
2- https://pubs.acs.org/doi/10.1021/bi201710q
I would be glad to listen to any of the ideas you have to make these modified sugars. Thanks again for your time and cooperation.
First of all, thanks a lot for your earnest response. With regards to your first query, I am not sure if there are any available software tools for sugar mutations. However, please let me know if you find/are aware of any such tools for sugar mutations. It would be of great help to me.
' Cannot you do it manually? '- I can do it manually but i will have to worry about the dihedral angles and bond length in the case of the mutated sugars and it might be inconsistent with the conformation that i have taken from the fiber model from web x3dna 2.0. So, O2'-C2'-C3'-C4' dihedral is the main cause of my concern.
' How do you consider the sugar conformations (C3'-endo vs C2'-endo) after adding O2' ?'- Ideally, I would like to have the sugar conformations unchanged for the modified bases after addition of O2', if there are no steric clashes. Then, I want to see what changes come up over time to these forcibly retained bases, through MD simulations.
' Do you have a concrete example of such mutations? '- Yes, there are many examples of such mutations in literature. Please go through either of these links to have a rough idea of what I am trying to study:
1- https://onlinelibrary.wiley.com/doi/full/10.1002/cbic.201600385
2- https://pubs.acs.org/doi/10.1021/bi201710q
I would be glad to listen to any of the ideas you have to make these modified sugars. Thanks again for your time and cooperation.