You can find any additional information you require there. Of course, the mutated amino acid must be different than the residue to mutate. Note: The FoldX website has very good documentation for each FoldX command. PDB by ID: The first parameter is the Protein Data Bank (PDB) 1 code. The second file has additional information (the individual values used to calculate total change in free energy). (It can also output the mutated pdb file by setting -out-pdb=true.)Įither of those files can be used to determine change in free energy upon mutation (ddg ~ delta delta g). PS_1AJY_Repair_MA30d_scanning_output.txt.To initiate a mutation, simply click on the mutation tool located at the top of the display window. This can be very useful to quickly evaluate the putative effect of a mutaion before actually doing the lab work. Note: 'd' means try mutate the residue to 24 different amino acids or, you can specify any of those 24, including the standard 20. Mutating Amino-Acids Swiss-PdbViewer allows to browse a rotamer library in order to change amino acids sidechains. FoldX -command=PositionScan -pdb=1AJY_Repair.pdb -output-file=1AJY_Repair_MA30d -out-pdb=false -positions=MA30d More advanced mutations can be done with the BuildModel command. PositionScan can mutate to any amino acid. Then, either use AlaScan or PositionScan to mutate. It may not work as well as molecular dynamics software, but for your simple task, it is a reasonable solution.įirst, repair your structure (since, usually PDBs are not energetically optimised, so you could get better energy anyway without doing this): FoldX -command=repairpdb -pdb=1AJY.pdb It can do both of what you want - the mutation and energy optimisation. It is very easy to use and state of the art (it is the main competitor to expensive commercial software). I would recommend you try the FoldX mutation engine.
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