binder design

1.0 binder

1.1 about rosetta ddG

In the binding molecules, rosetta ddG<-40 is used as the screening condition. I want to know how this part is calculated. I can't find the relevant script. Is the output of protein mpnn used as the mutation and the initial Gly skeleton used as the comparison?

1.2 about pae_interaction

In my design work, I only used about 10 skeletons and got many sequences with pae_interaction<10, which confused me

1.2.1 for example out.sc

SCORE: binder_aligned_rmsd pae_binder pae_interaction pae_target plddt_binder plddt_target plddt_total target_aligned_rmsd time description
SCORE: 0.592 3.476 8.182 9.139 85.556 74.229 78.750 1.542 83.551 design_ppi_0_dldesign_0_af2pred
SCORE: 0.930 5.717 13.545 9.519 70.353 68.488 69.232 1.716 7.883 design_ppi_0_dldesign_1_af2pred
SCORE: 0.885 2.977 7.414 8.460 87.404 76.294 80.728 1.496 7.833 design_ppi_0_dldesign_2_af2pred
SCORE: 2.054 7.001 13.005 9.961 66.544 65.600 65.977 2.215 7.828 design_ppi_0_dldesign_3_af2pred
SCORE: 0.780 3.225 7.507 8.800 87.345 76.268 80.564 1.516 82.688 design_ppi_1_dldesign_0_af2pred
SCORE: 1.126 3.107 6.819 7.912 88.812 79.364 83.028 1.721 7.771 design_ppi_1_dldesign_1_af2pred
SCORE: 0.687 3.506 7.869 9.009 85.927 76.209 79.978 1.124 7.590 design_ppi_1_dldesign_2_af2pred
SCORE: 0.715 3.452 7.688 9.015 87.045 76.115 80.354 1.181 7.384 design_ppi_1_dldesign_3_af2pred
SCORE: 0.753 2.880 12.781 10.139 82.801 66.895 72.926 2.832 83.061 design_ppi_2_dldesign_0_af2pred
SCORE: 4.713 6.647 17.966 10.022 67.370 64.381 65.514 7.578 7.448 design_ppi_2_dldesign_1_af2pred
SCORE: 0.585 2.578 8.057 9.152 87.885 74.091 79.321 1.455 7.893 design_ppi_2_dldesign_2_af2pred
SCORE: 5.456 8.717 21.638 9.816 66.661 65.740 66.089 10.151 7.169 design_ppi_2_dldesign_3_af2pred
SCORE: 1.223 3.388 8.150 9.291 88.463 74.946 80.523 2.229 83.386 design_ppi_3_dldesign_0_af2pred
SCORE: 1.084 3.811 8.760 9.382 86.099 73.772 78.858 2.097 8.280 design_ppi_3_dldesign_1_af2pred
SCORE: 1.239 3.116 7.614 8.654 88.546 76.457 81.444 2.109 8.154 design_ppi_3_dldesign_2_af2pred
SCORE: 1.114 4.012 8.458 9.047 85.521 74.985 79.332 1.853 8.049 design_ppi_3_dldesign_3_af2pred
SCORE: 30.849 13.027 17.585 9.168 74.318 72.932 73.446 45.073 75.428 design_ppi_4_dldesign_0_af2pred
SCORE: 32.573 9.324 14.422 8.683 87.638 76.735 80.771 47.214 7.665 design_ppi_4_dldesign_1_af2pred
SCORE: 1.036 3.308 8.186 9.418 86.905 74.156 78.876 1.598 6.808 design_ppi_4_dldesign_2_af2pred
SCORE: 1.055 3.597 8.303 9.421 85.697 73.982 78.319 1.433 7.470 design_ppi_4_dldesign_3_af2pred
SCORE: 7.624 10.777 24.481 9.155 52.892 63.817 59.142 12.690 84.331 design_ppi_5_dldesign_0_af2pred
SCORE: 9.163 11.825 26.501 8.199 51.977 69.317 61.897 19.410 8.484 design_ppi_5_dldesign_1_af2pred
SCORE: 7.530 11.392 24.215 9.933 53.076 61.796 58.064 13.101 8.735 design_ppi_5_dldesign_2_af2pred
SCORE: 2.680 7.861 13.244 9.600 68.653 68.895 68.791 3.466 9.189 design_ppi_5_dldesign_3_af2pred
SCORE: 1.138 4.400 9.203 9.374 81.033 72.488 75.802 1.893 7.801 design_ppi_6_dldesign_0_af2pred
SCORE: 1.178 4.334 9.951 9.740 80.572 70.593 74.463 1.821 7.961 design_ppi_6_dldesign_1_af2pred
SCORE: 1.221 4.154 9.192 9.283 82.260 72.068 76.021 1.859 7.870 design_ppi_6_dldesign_2_af2pred
SCORE: 9.541 13.511 20.715 10.050 63.012 65.187 64.343 14.675 8.523 design_ppi_6_dldesign_3_af2pred
...
SCORE: 1.000 4.023 8.681 9.366 83.065 72.978 77.085 1.877 7.684 design_ppi_9_dldesign_3_af2pred
...

No script or test is named; start by locating the workflow that produces the reported out.sc scores and the calculations for rosetta ddG and pae_interaction. Document which inputs are compared and how each metric is calculated, using the listed ProteinMPNN, Gly skeleton, and AF2 outputs as context; done means the issue's questions are answered with reproducible references.