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Fixing template issues
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@RomFas
RomFas committed Feb 3, 2023
1 parent e45df85 commit 65baa90
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -62,6 +62,7 @@ python New_APE-Gen.py ARpSEpTEVIpYS HLA-A*11:01 --verbose --score_with_openmm
### Main Workflow:

#### Minor issues:
- Motifs from openvax that are identical in regards to alleles do not exist as is in the file. I need to match e.g. `A*02:17` to `A*02:01` correctly.
- See if there is a cleaner way to define the anchors for cases not found in PMBEC.
- Add MHCFlurry motifs prediction in the workflow (you can take those from the notebooks created)
- Add pdb2pqr for protonation.
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2 changes: 1 addition & 1 deletion helper_files/Proper_files/Template_DB.csv
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Expand Up @@ -395,7 +395,7 @@ pdb_code,MHC,peptide,peptide_length,Major_anchors,Secondary_anchors
4U1N.pdb,HLA-B*42:02,RPQVPLRPM,9,"2,9","2,9"
4U1S.pdb,HLA-B*81:01,FPRPWLHGL,9,"2,9","1,2,3,9"
4U6Y.pdb,HLA-A*02:01,FLNKDLEVDGHFVTM,15,"2,15","15,2,6"
4WJ5.pdb,HLA-A*02:01,GVAGIGILTA,10,"2,10","1,2,7,10"
4WJ5.pdb,HLA-A*02:01,GAAGIGILTA,10,"2,10","1,2,7,10"
4WU5.pdb,HLA-A*24:02,RYPLTFGW,8,"2,8","5,2,3,8"
4WU7.pdb,HLA-A*24:02,RFPLTFGW,8,"2,8","2,3,8"
4XXC.pdb,HLA-B*18:01,DELEIKAY,8,"2,8","1,5,2,8"
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16 changes: 8 additions & 8 deletions new_templates_final/3FT2.pdb
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Expand Up @@ -2714,16 +2714,16 @@ ATOM 2337 CG LEU C 2 -12.840 7.374 7.370 1.00 23.64 C
ATOM 2338 CD1 LEU C 2 -12.814 8.541 6.422 1.00 25.77 C
ATOM 2339 CD2 LEU C 2 -11.573 7.353 8.232 1.00 23.77 C
ATOM 2340 C ARG C 3 -16.979 9.404 11.039 1.00 22.65 C
ATOM 2341 O1 ARG C 3 -16.387 9.963 10.085 1.00 24.20 O
ATOM 2341 O ARG C 3 -16.387 9.963 10.085 1.00 24.20 O
ATOM 2342 CA ARG C 3 -16.218 8.437 11.911 1.00 19.53 C
ATOM 2343 N ARG C 3 -15.317 7.596 11.127 1.00 19.20 N
ATOM 2344 C3 ARG C 3 -15.428 9.245 12.942 1.00 18.86 C
ATOM 2345 C4 ARG C 3 -14.839 8.373 14.035 1.00 20.52 C
ATOM 2346 C5 ARG C 3 -14.077 9.277 15.007 1.00 18.95 C
ATOM 2347 N6 ARG C 3 -13.202 8.533 15.901 1.00 20.86 N
ATOM 2348 C7 ARG C 3 -13.596 7.853 16.970 1.00 22.78 C
ATOM 2349 N2 ARG C 3 -12.767 7.327 17.700 1.00 23.36 N
ATOM 2350 N8 ARG C 3 -14.903 7.772 17.230 1.00 23.47 N
ATOM 2344 CB ARG C 3 -15.428 9.245 12.942 1.00 18.86 C
ATOM 2345 CG ARG C 3 -14.839 8.373 14.035 1.00 20.52 C
ATOM 2346 CD ARG C 3 -14.077 9.277 15.007 1.00 18.95 C
ATOM 2347 NE ARG C 3 -13.202 8.533 15.901 1.00 20.86 N
ATOM 2348 CZ ARG C 3 -13.596 7.853 16.970 1.00 22.78 C
ATOM 2349 NH1 ARG C 3 -12.767 7.327 17.700 1.00 23.36 N
ATOM 2350 NH2 ARG C 3 -14.903 7.772 17.230 1.00 23.47 N
ATOM 2351 N ASP C 4 -18.209 9.696 11.462 1.00 29.41 N
ATOM 2352 CA ASP C 4 -19.072 10.699 10.764 1.00 33.88 C
ATOM 2353 C ASP C 4 -18.493 12.110 10.804 1.00 35.81 C
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18 changes: 8 additions & 10 deletions new_templates_final/4WJ5.pdb
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Expand Up @@ -3468,13 +3468,11 @@ ATOM 2439 O GLY C 1 5.963 -7.295 13.774 1.00 16.74 O
ATOM 2440 C GLY C 1 6.370 -6.524 12.872 1.00 15.82 C
ATOM 2441 CA GLY C 1 7.348 -6.999 11.790 1.00 14.11 C
ATOM 2442 N GLY C 1 8.358 -5.968 11.483 1.00 16.33 N
ATOM 2443 N VAL C 2 5.838 -5.322 12.824 1.00 11.79 N
ATOM 2445 CA VAL C 2 4.768 -4.411 13.274 1.00 13.60 C
ATOM 2447 CB VAL C 2 5.098 -3.401 14.347 1.00 13.95 C
ATOM 2449 CG VAL C 2 5.639 -2.132 13.703 1.00 13.46 C
ATOM 2451 CD VAL C 2 4.900 -0.918 14.194 1.00 11.91 C
ATOM 2453 C VAL C 2 3.637 -5.381 13.588 1.00 11.92 C
ATOM 2455 O VAL C 2 3.212 -6.029 12.648 1.00 10.65 O
ATOM 2443 N ALA C 2 5.838 -5.322 12.824 1.00 11.79 N
ATOM 2445 CA ALA C 2 4.768 -4.411 13.274 1.00 13.60 C
ATOM 2447 CB ALA C 2 5.098 -3.401 14.347 1.00 13.95 C
ATOM 2453 C ALA C 2 3.637 -5.381 13.588 1.00 11.92 C
ATOM 2455 O ALA C 2 3.212 -6.029 12.648 1.00 10.65 O
ATOM 2457 N ALA C 3 3.032 -5.547 14.780 1.00 21.01 N
ATOM 2458 CA ALA C 3 1.791 -6.322 14.836 1.00 19.73 C
ATOM 2459 C ALA C 3 0.705 -5.576 14.030 1.00 20.55 C
Expand Down Expand Up @@ -3522,8 +3520,8 @@ ATOM 2500 CG2 THR C 9 -7.881 3.296 21.154 1.00 30.50 C
ATOM 2501 CB ALA C 10 -6.523 1.250 27.477 1.00 23.52 C
ATOM 2502 CA ALA C 10 -7.480 0.871 26.416 1.00 22.73 C
ATOM 2503 N ALA C 10 -7.150 1.188 25.079 1.00 21.92 N
ATOM 2504 C ALA C 10 -8.888 0.926 26.864 1.00 24.36 C
ATOM 2505 OXT ALA C 10 -9.342 0.400 27.884 1.00 29.59 O
ATOM 2506 O ALA C 10 -9.637 1.728 26.166 1.00 26.02 O
ATOM 2504 C ALA C 10 -8.888 0.926 26.864 1.00 24.36 C
ATOM 2505 O ALA C 10 -9.637 1.728 26.166 1.00 26.02 O
ATOM 2506 OXT ALA C 10 -9.342 0.400 27.884 1.00 29.59 O
TER 2507 ALA C 10
END
10 changes: 5 additions & 5 deletions new_templates_final/5XS3.pdb
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Expand Up @@ -1039,11 +1039,11 @@ ATOM 463 O THR A 61 3.803 72.487 -4.007 1.00 15.82 O
ATOM 464 CB THR A 61 1.588 74.586 -5.384 1.00 18.52 C
ATOM 465 OG1 THR A 61 0.882 75.783 -5.029 1.00 19.05 O
ATOM 466 CG2 THR A 61 0.803 73.386 -4.864 1.00 18.37 C
ATOM 467 N GLN A 62 4.074 72.930 -6.196 1.00 15.81 N
ATOM 468 CA GLN A 62 4.735 71.654 -6.451 1.00 15.99 C
ATOM 469 C GLN A 62 5.950 71.471 -5.552 1.00 15.76 C
ATOM 470 O GLN A 62 6.191 70.373 -5.024 1.00 14.85 O
ATOM 471 CB GLN A 62 5.153 71.561 -7.918 1.00 16.21 C
ATOM 467 N ALA A 62 4.074 72.930 -6.196 1.00 15.81 N
ATOM 468 CA ALA A 62 4.735 71.654 -6.451 1.00 15.99 C
ATOM 469 C ALA A 62 5.950 71.471 -5.552 1.00 15.76 C
ATOM 470 O ALA A 62 6.191 70.373 -5.024 1.00 14.85 O
ATOM 471 CB ALA A 62 5.153 71.561 -7.918 1.00 16.21 C
ATOM 472 N LYS A 63 6.724 72.538 -5.353 1.00 15.44 N
ATOM 473 CA LYS A 63 7.921 72.404 -4.534 1.00 14.74 C
ATOM 474 C LYS A 63 7.584 72.288 -3.049 1.00 14.57 C
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