Hi everyone,<br><br>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.
<br>My approach to do this is 1) mutate using MODELLER, <br>2) check the structure with something like PROCKECK (although since I am just mutating one residue, this doesn't seem important/useful), <br>3) align the resulting structure from MODELLER with the original and paste the DNA
<br>4) check for clashes with PROCHECK, and <br>5) do MD to see whether the model is feasible/calculate free energy of binding. <br>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?<br><br>Thanks a lot for your help,<br>Esther<br clear="all"><br>-- <br>Esther Caballero-Manrique
<br>Unit of Cancer Pathology<br>Center for Excellence in Research on Aging<br>University "G. D' Annunzio"<br>Via Colle dell' Ara<br>66013 Chieti Scalo (Chieti), Italy