Dear Biostar members,
I have an existing PDB structure for which I would like to generate a new, reliable, model/structure by phosphorylating the residues in-silico.
Could you kindly give me advice on how one would proceed to do this?
I would appreciate any advice on particular protein modelling tools, program modules or functions, or a starting framework of how this gets done specifically for protein phosphorylation. Any tutorials or books on the subject would also be helpful!
I have been browsing online and my general understanding is that once a model is generated using a 3D modelling program, the model should be run through a force field (CHARMM or GROMACS)...I am not sure whether this is necessary or whether the validation of the model can be done using the standard modelling tools.
My question overlaps with how to generate a model from mutating a residue in silico, which is something I am also trying to do, so any thoughts in that direction are also welcome!
My apologies if this has been posted elsewhere. Thank you in advance!
Best wishes, Deena
Have you looked into using Rosetta for this? It sounds like a problem of re-doing the modelling using the un modified structure as a template.
However you solve this, be sceptical of the results. There are known structures of phosphorylated proteins that are quite different to the unphosphorylated form - and others with very little difference at all. In other words, the effect of phosphorylation on structure is highly variable and difficult to predict.