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tommyhuangthu / EvoEF

a fast and accurate physical energy function for predicting protein stability and protein-protein affinity changes upon amino-acid mutations
MIT License
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Mutating numbered antibody files #3

Open nieuwoudtmd opened 1 year ago

nieuwoudtmd commented 1 year ago

Hi,

When the antibody is numbered to a specific scheme, for example Chothia numbering scheme, you can expect the pdb to be numbered like this:

ATOM 24170 N ASN H 82A 219.106 150.023 123.621 1.00281.57 N
ATOM 24171 CA ASN H 82A 220.131 149.195 123.007 1.00281.57 C
ATOM 24172 C ASN H 82A 219.503 148.052 122.218 1.00281.57 C
ATOM 24173 O ASN H 82A 218.352 147.668 122.441 1.00281.57 O
ATOM 24174 CB ASN H 82A 221.083 148.644 124.070 1.00281.57 C
ATOM 24175 CG ASN H 82A 221.611 149.725 124.991 1.00281.57 C
ATOM 24176 OD1 ASN H 82A 222.071 150.772 124.537 1.00281.57 O
ATOM 24177 ND2 ASN H 82A 221.539 149.481 126.292 1.00281.57 N
ATOM 24178 N SER H 82B 220.287 147.507 121.288 1.00283.06 N
ATOM 24179 CA SER H 82B 219.867 146.405 120.422 1.00283.06 C
ATOM 24180 C SER H 82B 218.641 146.797 119.597 1.00283.06 C
ATOM 24181 O SER H 82B 217.557 146.224 119.719 1.00283.06 O
ATOM 24182 CB SER H 82B 219.599 145.137 121.234 1.00283.06 C
ATOM 24183 OG SER H 82B 218.292 145.162 121.777 1.00283.06 O
ATOM 24184 N LEU H 82C 218.839 147.806 118.753 1.00286.83 N
ATOM 24185 CA LEU H 82C 217.771 148.287 117.888 1.00286.83 C
ATOM 24186 C LEU H 82C 217.421 147.253 116.826 1.00286.83 C
ATOM 24187 O LEU H 82C 218.298 146.643 116.210 1.00286.83 O
ATOM 24188 CB LEU H 82C 218.186 149.603 117.236 1.00286.83 C
ATOM 24189 CG LEU H 82C 218.703 150.577 118.287 1.00286.83 C
ATOM 24190 CD1 LEU H 82C 219.295 151.821 117.674 1.00286.83 C
ATOM 24191 CD2 LEU H 82C 217.569 150.923 119.213 1.00286.83 C

After running EvoEF to build a mutant it removes the A, B, C and keeps the residue id:

ATOM 29502 N ASN H 82 219.106 150.023 123.621 1 N ATOM 29503 H ASN H 82 218.521 149.543 124.273 1 H ATOM 29504 CA ASN H 82 220.131 149.195 123.007 1 C ATOM 29505 CB ASN H 82 221.083 148.644 124.070 1 C ATOM 29506 CG ASN H 82 221.611 149.725 124.991 1 C ATOM 29507 OD1 ASN H 82 222.071 150.772 124.537 1 O ATOM 29508 ND2 ASN H 82 221.539 149.481 126.292 1 N ATOM 29509 1HD2 ASN H 82 221.872 150.188 126.909 1 H ATOM 29510 2HD2 ASN H 82 221.136 148.631 126.618 1 H ATOM 29511 C ASN H 82 219.503 148.052 122.218 1 C ATOM 29512 O ASN H 82 218.352 147.668 122.441 1 O ATOM 29513 N SER H 82 220.287 147.507 121.288 1 N ATOM 29514 H SER H 82 221.221 147.823 121.125 1 H ATOM 29515 CA SER H 82 219.867 146.405 120.422 1 C ATOM 29516 CB SER H 82 219.599 145.137 121.234 1 C ATOM 29517 OG SER H 82 218.292 145.162 121.777 1 O ATOM 29518 HG SER H 82 218.094 144.267 122.081 1 H ATOM 29519 C SER H 82 218.641 146.797 119.597 1 C ATOM 29520 O SER H 82 217.557 146.224 119.719 1 O ATOM 29521 N LEU H 82 218.839 147.806 118.753 1 N ATOM 29522 H LEU H 82 219.702 148.295 118.649 1 H ATOM 29523 CA LEU H 82 217.771 148.287 117.888 1 C ATOM 29524 CB LEU H 82 218.186 149.603 117.236 1 C ATOM 29525 CG LEU H 82 218.703 150.577 118.287 1 C ATOM 29526 CD1 LEU H 82 219.295 151.821 117.674 1 C ATOM 29527 CD2 LEU H 82 217.569 150.923 119.213 1 C ATOM 29528 C LEU H 82 217.421 147.253 116.826 1 C ATOM 29529 O LEU H 82 218.298 146.643 116.210 1 O

I thought I'd bring this to your attention. We deal with the issue by renumbering the pdb from 1 and mapping all mutations back.