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The DDG process consists of two steps. The first step is to relax the PDB using the ddg-relax API. This step must be performed only once for each structure prior to running mutagenesis experiments with the ddg API. If multiple rounds of mutagenesis experiments are to be performed on a single protein, the same relaxed model should be used as the input for each relaxed protein. In the second step of the DDG process the TSV mutation file (described below) is parsed to generate a list of all specified single point mutations. Each one of these mutations is simulated via the Cartesian DDG protocol and DDG scores are reported for each mutation.

Inputs (DDG Relax)

• pdb-file

  • A PDB file

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• pdb-file

  • must be a PDB which has been run through the ddg-relax endpoint described above

• Optional - mutations-file

  • Tab Separated Value (TSV)-formatted file containing mutations. To create an empty mutations file from an input PDB, run:
    cyrus prepare mutations <pdb-file> --output-dir <output-dir>

  • Each row can contain one or many mutations, in the format D or DMG. For example, The TSV file below would allow residue 1 to mutate to Aspartic Acid, Glycine, or remain un-mutated as Methionine, and would not allow any mutations for residue 2:run DDG on M1D, M1G and Q2T and would report scores for all 3 of those mutations. The mutations are performed separate from each-other (ie the M1D and M1G mutations are not performed at the same time.)

  • Do not supply the native residue as a mutation, that doesn’t make sense.

position	original_residue	mutation 
1	M DMGDG
2	Q QT

• Optional - all-mutations mode

  • you can omit an input mutations-file and instead run in all-mutations mode, where all mutations at each position will be selected

• Optional - dump-pdb mode

  • run with this flag to output the PDB for each mutation as well as the score

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