Does DDGun handles dimers or double mutants?

[adrinesouza]

Hello DDG people.

I have run the script successfully for the wild-type protein of AGXT using 1h0c.pdb

But now, I need to evaluate the DDG scores for triple mutants. In the minor allele background that has SNPs on residues 11 and 340. The only PDB structure for this has A and B chains: 7ns7.pdb

How can I surpass this error: ./ddgun_3d.py agxt/7ns7.pdb A agxt/7ns7.muts ERROR: Incorrect PDB file agxt/7ns7.pdb. ./ddgun_3d.py agxt/7ns7.pdb A agxt/7ns7.muts ERROR: Incorrect PDB file agxt/7ns7.pdb. ./ddgun_seq.py agxt/7ns7.pdb.A.fasta agxt/7ns7.muts -o /home/rothlab/adesouza/ddgun/agxt/AGXT_minor_ddGun.csv ERROR: Incorrect sequence file agxt/7ns7.pdb.A.fasta.

Thank you

[ecapriotti]

Hello, can you provide more details about the mutation file? In principle if the mutation is correct it should work. Many thanks Emidio

[adrinesouza]

Yes,

I used the same mutation file I used previously with the wild-type background (pdb: 1h0c)

But I modified the initial residue for the residues 11 and 340, that are different in the minor allele (7ns7).

For those, instead of P11(Mutant residue), I changed these variants to L11(Mutant residue) and the same for I340(Mutant residue) that became M340(Mutant residue).

The files I used are attached. AGXT_minor_DDG.zip

I have been using the Biofold website to get scores for 100 mutants at a time. But I noticed the output is different than the one I go using the script for the major allele.

Old results using the script for 1h0c:

SEQFILE | VARIANT | S_DDG[SEQ] | T_DDG[SEQ] | STABILITY[SEQ]

1h0c.pdb.A.fasta P21C -0.1 -0.1 Decrease 1h0c.pdb.A.fasta P21D -0.1 -0.1 Decrease 1h0c.pdb.A.fasta P21E -0.1 -0.1 Decrease 1h0c.pdb.A.fasta P21F 0 0 Neutral

Using the website for 7ns7 (checking both seq and 3d): mutation | kyte-doolittle | blosum | profile | s3d | rsa | ΔΔG[SEQ] / Stability | ΔΔG[3D] / Stability L25R | -0.312 | -0.728 | 0.328 | 0.373 | 19 | -0.4 ↓ | -0.4 ↓ G109V | 0.22 | -3.891 | -3.505 | -2.428 | 1 | 0.4 ↑ | 1.2 ↑ R111Q | 0.701 | -0.498 | 1.258 | 0.371 | 42 | -0.5 ↓ | -0.3 ↓ G161R | 0.311 | -9.294 | -2.378 | -1.642 | 4 | -1.7 ↓ | -0.6 ↓

Now using the website for 7ns7 (checking only seq): mutation | kyte-doolittle | blosum | profile | ΔΔG[SEQ] / Stability L25R | -0.16 | -0.362 | 0.2 | -0.2 ↓ G109V | 0.21 | -2.496 | -3.087 | 0.6 ↑ R111Q | 0.43 | -0.006 | 0.932 | -0.3 ↓ G161R | 0.311 | -8.762 | -2.336 | -1.5 ↓

I would appreciate getting some insight about these differences in scores fro the script to the website so I can compare the same thing.