Hi everyone, I am new to mutagenesis studies, so I was wondering if I could get some input on my approach. My task involves mutagenizing a residue (with all 19 possibilities) in a protein that binds DNA, and then deciding whether the resulting structure is physically acceptable. My approach to do this is 1) mutate using MODELLER, 2) check the structure with something like PROCKECK (although since I am just mutating one residue, this doesn't seem important/useful), 3) align the resulting structure from MODELLER with the original and paste the DNA 4) check for clashes with PROCHECK, and 5) do MD to see whether the model is feasible/calculate free energy of binding. Obviously all steps are easy and fast except the last one, and my question is, does anyone think that step 5 is overdoing it if one just needs to know whether a structure is feasible (i.e., I am not using MD for refinement, but as a check of the feasibility of the complex)? Does anyone have a better/easier way to do this?
Thanks a lot for your help, Esther -- Esther Caballero-Manrique Unit of Cancer Pathology Center for Excellence in Research on Aging University "G. D' Annunzio" Via Colle dell' Ara 66013 Chieti Scalo (Chieti), Italy
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