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explore the conformational changes occuring in riboswitches in the presence and absence of ligand
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23 months ago

hi I am new in dynamics field, i want to explore the conformational changes occuring in riboswitches in the presence and absence of ligand.need help regarding study materials guidance being a beginner. currently thinking of using GROMACS with AMBER force field. looking forward for reply.

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You know that the whole molecule changes upon ligand-sensing and -binding, right? That would require quite a bit of processing power to simulate. I might be wrong here, but last time I checked there were no crystal structures of a riboswitch in unbound state, so you don't even have a proper starting structure (unless you just build a linear chain of nucleotides). Please keep us posted how you get on, would be interesting to see.

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very few structures are present in unbound form in PDB, but if we build the 3d structure with RNAComposer in case the structure is not available, will it be fine ?

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I don't know how good RNAComposer is. Given that it comes from the Poznan groups, I would say it will be pretty good. However, I am not sure that secondary structure prediction (which is a requirement for RNAComposer) has improved much in the past decade. Also, if your riboswitch contains an unknown structural motif (not so likely for RNA, but not impossible), then the homology modeling will fail to provide something adequate. I would not rely on modeling an unbound structure for simulation purposes, but then I have been out of the field for a while, so maybe I'm wrong.

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