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Merge pull request #73 from HannesStark/add-antibody-examples

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Add antibody scaffold examples
This commit is contained in:
Tim O'Donnell
2025-11-20 14:04:31 -05:00
committed by GitHub
parent 540234e9fb eb201df2ce
commit 527762d6c8
30 changed files with 242075 additions and 0 deletions
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10077
example/antibody_scaffolds/adalimumab.6cr1.cif Normal file
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example/antibody_scaffolds/adalimumab.6cr1.yaml Normal file
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# adalimumab 6cr1
# Target: TNF/TNFA
# Heavy chain (label not auth): B
# Light chain (label not auth): A
# Full heavy chain sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAITWNSGHIDYADSVEGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCAKVSYLSTASSLDYWGQGTLVTVSSASTKGPTVKILQSICDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCAHHHHHH
# Full light chain sequence: DIQMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQRYNRAPYTFGQGTKVEIKRTVAAPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSGKKCA
# Variable heavy region: 1 - 121
# Variable light region: 1 - 107
# Heavy CDRs: GFTFDDY TWNSGH VSYLSTASSLDY
# Light CDRs: RASQGIRNYLA AASTLQS QRYNRAPYT
#
path: adalimumab.6cr1.cif
include:
- chain:
id: B # heavy
res_index: 1..121
- chain:
id: A # light
res_index: 1..107
design:
- chain:
id: B
res_index: 26..32,52..57,99..110
- chain:
id: A
res_index: 24..34,50..56,89..97
structure_groups:
- group:
id: B
res_index: 26..32,52..57,99..110
visibility: 0
- group:
id: A
res_index: 24..34,50..56,89..97
visibility: 0
exclude:
- chain:
id: B
res_index: 26..32
- chain:
id: B
res_index: 52..57
- chain:
id: B
res_index: 99..110
- chain:
id: A
res_index: 24..34
- chain:
id: A
res_index: 50..56
- chain:
id: A
res_index: 89..97
design_insertions:
- insertion:
id: B
res_index: 26
num_residues: 7..9
- insertion:
id: B
res_index: 52
num_residues: 5..8
- insertion:
id: B
res_index: 99
num_residues: 3..21
- insertion:
id: A
res_index: 24
num_residues: 10..17
- insertion:
id: A
res_index: 50
num_residues: 7
- insertion:
id: A
res_index: 89
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: B
- chain:
id: A

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example/antibody_scaffolds/belimumab.5y9k.cif Normal file
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example/antibody_scaffolds/belimumab.5y9k.yaml Normal file
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# belimumab 5y9k
# Target: TNFSF13B/CD257/BAFF
# Heavy chain (label not auth): B
# Light chain (label not auth): A
# Full heavy chain sequence: QVQLQQSGAEVKKPGSSVRVSCKASGGTFNNNAINWVRQAPGQGLEWMGGIIPMFGTAKYSQNFQGRVAITADESTGTASMELSSLRSEDTAVYYCARSRDLLLFPHHALSPWGRGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH
# Full light chain sequence: SSELTQDPAVSVALGQTVRVTCQGDSLRSYYASWYQQKPGQAPVLVIYGKNNRPSGIPDRFSGSSSGNTASLTITGAQAEDEADYYCSSRDSSGNHWVFGGGTELTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
# Variable heavy region: 1 - 123
# Variable light region: 1 - 108
# Heavy CDRs: GGTFNNN IPMFGT SRDLLLFPHHALSP
# Light CDRs: QGDSLRSYYAS GKNNRPS SSRDSSGNHWV
#
path: belimumab.5y9k.cif
include:
- chain:
id: B # heavy
res_index: 1..123
- chain:
id: A # light
res_index: 1..108
design:
- chain:
id: B
res_index: 26..32,52..57,99..112
- chain:
id: A
res_index: 23..33,49..55,88..98
structure_groups:
- group:
id: B
res_index: 26..32,52..57,99..112
visibility: 0
- group:
id: A
res_index: 23..33,49..55,88..98
visibility: 0
exclude:
- chain:
id: B
res_index: 26..32
- chain:
id: B
res_index: 52..57
- chain:
id: B
res_index: 99..112
- chain:
id: A
res_index: 23..33
- chain:
id: A
res_index: 49..55
- chain:
id: A
res_index: 88..98
design_insertions:
- insertion:
id: B
res_index: 26
num_residues: 7..9
- insertion:
id: B
res_index: 52
num_residues: 5..8
- insertion:
id: B
res_index: 99
num_residues: 3..21
- insertion:
id: A
res_index: 23
num_residues: 10..17
- insertion:
id: A
res_index: 49
num_residues: 7
- insertion:
id: A
res_index: 88
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: B
- chain:
id: A

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example/antibody_scaffolds/crenezumab.5vzy.cif Normal file
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example/antibody_scaffolds/crenezumab.5vzy.yaml Normal file
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# crenezumab 5vzy
# Target: Abeta
# Heavy chain (label not auth): A
# Light chain (label not auth): B
# Full heavy chain sequence: EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYGMSWVRQAPGKGLELVASINSNGGSTYYPDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCASGDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
# Full light chain sequence: DIVMTQSPLSLPVTPGEPASISCRSSQSLVYSNGDTYLHWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCSQSTHVPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
# Variable heavy region: 1 - 112
# Variable light region: 1 - 112
# Heavy CDRs: GFTFSSY NSNGGS GDY
# Light CDRs: RSSQSLVYSNGDTYLH KVSNRFS SQSTHVPWT
#
path: crenezumab.5vzy.cif
include:
- chain:
id: A # heavy
res_index: 1..112
- chain:
id: B # light
res_index: 1..112
design:
- chain:
id: A
res_index: 26..32,52..57,99..101
- chain:
id: B
res_index: 24..39,55..61,94..102
structure_groups:
- group:
id: A
res_index: 26..32,52..57,99..101
visibility: 0
- group:
id: B
res_index: 24..39,55..61,94..102
visibility: 0
exclude:
- chain:
id: A
res_index: 26..32
- chain:
id: A
res_index: 52..57
- chain:
id: A
res_index: 99..101
- chain:
id: B
res_index: 24..39
- chain:
id: B
res_index: 55..61
- chain:
id: B
res_index: 94..102
design_insertions:
- insertion:
id: A
res_index: 26
num_residues: 7..9
- insertion:
id: A
res_index: 52
num_residues: 5..8
- insertion:
id: A
res_index: 99
num_residues: 3..21
- insertion:
id: B
res_index: 24
num_residues: 10..17
- insertion:
id: B
res_index: 55
num_residues: 7
- insertion:
id: B
res_index: 94
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: A
- chain:
id: B

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example/antibody_scaffolds/dupilumab.6wgb.cif Normal file
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example/antibody_scaffolds/dupilumab.6wgb.yaml Normal file
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# dupilumab 6wgb
# Target: IL4R/CD124
# Heavy chain (label not auth): A
# Light chain (label not auth): B
# Full heavy chain sequence: EVQLVESGGGLEQPGGSLRLSCAGSGFTFRDYAMTWVRQAPGKGLEWVSSISGSGGNTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRLSITIRPRYYGLDVWGQGTTVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGHHHHHH
# Full light chain sequence: DIVMTQSPLSLPVTPGEPASISCRSSQSLLYSIGYNYLDWYLQKSGQSPQLLIYLGSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGFYYCMQALQTPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
# Variable heavy region: 1 - 125
# Variable light region: 1 - 112
# Heavy CDRs: GFTFRDY SGSGGN DRLSITIRPRYYGLDV
# Light CDRs: RSSQSLLYSIGYNYLD LGSNRAS MQALQTPYT
#
path: dupilumab.6wgb.cif
include:
- chain:
id: A # heavy
res_index: 1..125
- chain:
id: B # light
res_index: 1..112
design:
- chain:
id: A
res_index: 26..32,52..57,99..114
- chain:
id: B
res_index: 24..39,55..61,94..102
structure_groups:
- group:
id: A
res_index: 26..32,52..57,99..114
visibility: 0
- group:
id: B
res_index: 24..39,55..61,94..102
visibility: 0
exclude:
- chain:
id: A
res_index: 26..32
- chain:
id: A
res_index: 52..57
- chain:
id: A
res_index: 99..114
- chain:
id: B
res_index: 24..39
- chain:
id: B
res_index: 55..61
- chain:
id: B
res_index: 94..102
design_insertions:
- insertion:
id: A
res_index: 26
num_residues: 7..9
- insertion:
id: A
res_index: 52
num_residues: 5..8
- insertion:
id: A
res_index: 99
num_residues: 3..21
- insertion:
id: B
res_index: 24
num_residues: 10..17
- insertion:
id: B
res_index: 55
num_residues: 7
- insertion:
id: B
res_index: 94
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: A
- chain:
id: B

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example/antibody_scaffolds/golimumab.5yoy.cif Normal file
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example/antibody_scaffolds/golimumab.5yoy.yaml Normal file
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# golimumab 5yoy
# Target: TNF/TNFA
# Heavy chain (label not auth): H
# Light chain (label not auth): E
# Full heavy chain sequence: SKLQVQLVESGGGVVQPGRSLRLSCAASGFIFSSYAMHWVRQAPGNGLEWVAFMSYDGSNKKYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDRGIAAGGNYYYYGMDVWGQGTTVTVSS
# Full light chain sequence: AGSEIVLTQSPATLSLSPGERATLSCRASQSVYSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPFTFGPGTKVDIKTSENLYFQ
# Variable heavy region: 4 - 129
# Variable light region: 4 - 111
# Heavy CDRs: GFIFSSY SYDGSN DRGIAAGGNYYYYGMDV
# Light CDRs: RASQSVYSYLA DASNRAT QQRSNWPPFT
#
path: golimumab.5yoy.cif
include:
- chain:
id: H # heavy
res_index: 4..129
- chain:
id: E # light
res_index: 4..111
design:
- chain:
id: H
res_index: 29..35,55..60,102..118
- chain:
id: E
res_index: 27..37,53..59,92..101
structure_groups:
- group:
id: H
res_index: 29..35,55..60,102..118
visibility: 0
- group:
id: E
res_index: 27..37,53..59,92..101
visibility: 0
exclude:
- chain:
id: H
res_index: 29..35
- chain:
id: H
res_index: 55..60
- chain:
id: H
res_index: 102..118
- chain:
id: E
res_index: 27..37
- chain:
id: E
res_index: 53..59
- chain:
id: E
res_index: 92..101
design_insertions:
- insertion:
id: H
res_index: 29
num_residues: 7..9
- insertion:
id: H
res_index: 55
num_residues: 5..8
- insertion:
id: H
res_index: 102
num_residues: 3..21
- insertion:
id: E
res_index: 27
num_residues: 10..17
- insertion:
id: E
res_index: 53
num_residues: 7
- insertion:
id: E
res_index: 92
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: H
- chain:
id: E

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example/antibody_scaffolds/guselkumab.4m6m.cif Normal file
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example/antibody_scaffolds/guselkumab.4m6m.yaml Normal file
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# guselkumab 4m6m
# Target: IL23A
# Heavy chain (label not auth): B
# Light chain (label not auth): A
# Full heavy chain sequence: EVQLVQSGAEVKKPGESLKISCKGSGYSFSNYWIGWVRQMPGKGLEWMGIIDPSNSYTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARWYYKPFDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH
# Full light chain sequence: QSVLTQPPSVSGAPGQRVTISCTGSSSNIGSGYDVHWYQQLPGTAPKLLIYGNSKRPSGVPDRFSGSKSGTSASLAITGLQSEDEADYYCASWTDGLSLVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
# Variable heavy region: 1 - 117
# Variable light region: 1 - 111
# Heavy CDRs: GYSFSNY DPSNSY WYYKPFDV
# Light CDRs: TGSSSNIGSGYDVH GNSKRPS ASWTDGLSLVV
#
path: guselkumab.4m6m.cif
include:
- chain:
id: B # heavy
res_index: 1..117
- chain:
id: A # light
res_index: 1..111
design:
- chain:
id: B
res_index: 26..32,52..57,99..106
- chain:
id: A
res_index: 23..36,52..58,91..101
structure_groups:
- group:
id: B
res_index: 26..32,52..57,99..106
visibility: 0
- group:
id: A
res_index: 23..36,52..58,91..101
visibility: 0
exclude:
- chain:
id: B
res_index: 26..32
- chain:
id: B
res_index: 52..57
- chain:
id: B
res_index: 99..106
- chain:
id: A
res_index: 23..36
- chain:
id: A
res_index: 52..58
- chain:
id: A
res_index: 91..101
design_insertions:
- insertion:
id: B
res_index: 26
num_residues: 7..9
- insertion:
id: B
res_index: 52
num_residues: 5..8
- insertion:
id: B
res_index: 99
num_residues: 3..21
- insertion:
id: A
res_index: 23
num_residues: 10..17
- insertion:
id: A
res_index: 52
num_residues: 7
- insertion:
id: A
res_index: 91
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: B
- chain:
id: A

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example/antibody_scaffolds/mab1.3h42.cif Normal file
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example/antibody_scaffolds/mab1.3h42.yaml Normal file
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# mab1 3h42
# Target: PCSK9
# Heavy chain (label not auth): D
# Light chain (label not auth): C
# Full heavy chain sequence: EVQLVESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLEWVSSISSSSSYISYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYFCARDYDFWSAYYDAFDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAADEVDHHHHHH
# Full light chain sequence: ESVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLISGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGSVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
# Variable heavy region: 1 - 123
# Variable light region: 1 - 111
# Heavy CDRs: GFTFSSY SSSSSY DYDFWSAYYDAFDV
# Light CDRs: TGSSSNIGAGYDVH GNSNRPS QSYDSSLSGSV
#
path: mab1.3h42.cif
include:
- chain:
id: D # heavy
res_index: 1..123
- chain:
id: C # light
res_index: 1..111
design:
- chain:
id: D
res_index: 26..32,52..57,99..112
- chain:
id: C
res_index: 23..36,52..58,91..101
structure_groups:
- group:
id: D
res_index: 26..32,52..57,99..112
visibility: 0
- group:
id: C
res_index: 23..36,52..58,91..101
visibility: 0
exclude:
- chain:
id: D
res_index: 26..32
- chain:
id: D
res_index: 52..57
- chain:
id: D
res_index: 99..112
- chain:
id: C
res_index: 23..36
- chain:
id: C
res_index: 52..58
- chain:
id: C
res_index: 91..101
design_insertions:
- insertion:
id: D
res_index: 26
num_residues: 7..9
- insertion:
id: D
res_index: 52
num_residues: 5..8
- insertion:
id: D
res_index: 99
num_residues: 3..21
- insertion:
id: C
res_index: 23
num_residues: 10..17
- insertion:
id: C
res_index: 52
num_residues: 7
- insertion:
id: C
res_index: 91
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: D
- chain:
id: C

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example/antibody_scaffolds/necitumumab.6b3s.cif Normal file
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example/antibody_scaffolds/necitumumab.6b3s.yaml Normal file
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# necitumumab 6b3s
# Target: EGFR
# Heavy chain (label not auth): B
# Light chain (label not auth): C
# Full heavy chain sequence: QVQLQESGPGLVKPSQTLSLTCTVSGGSISSGDYYWSWIRQPPGKGLEWIGYIYYSGSTDYNPSLKSRVTMSVDTSKNQFSLKVNSVTAADTAVYYCARVSIFGVGTFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
# Full light chain sequence: EIVMTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCHQYGSTPLTFGGGTKAEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGA
# Variable heavy region: 1 - 121
# Variable light region: 1 - 107
# Heavy CDRs: GGSISSGDY YYSGS VSIFGVGTFDY
# Light CDRs: RASQSVSSYLA DASNRAT HQYGSTPLT
#
path: necitumumab.6b3s.cif
include:
- chain:
id: B # heavy
res_index: 1..121
- chain:
id: C # light
res_index: 1..107
design:
- chain:
id: B
res_index: 26..34,54..58,100..110
- chain:
id: C
res_index: 24..34,50..56,89..97
structure_groups:
- group:
id: B
res_index: 26..34,54..58,100..110
visibility: 0
- group:
id: C
res_index: 24..34,50..56,89..97
visibility: 0
exclude:
- chain:
id: B
res_index: 26..34
- chain:
id: B
res_index: 54..58
- chain:
id: B
res_index: 100..110
- chain:
id: C
res_index: 24..34
- chain:
id: C
res_index: 50..56
- chain:
id: C
res_index: 89..97
design_insertions:
- insertion:
id: B
res_index: 26
num_residues: 7..9
- insertion:
id: B
res_index: 54
num_residues: 5..8
- insertion:
id: B
res_index: 100
num_residues: 3..21
- insertion:
id: C
res_index: 24
num_residues: 10..17
- insertion:
id: C
res_index: 50
num_residues: 7
- insertion:
id: C
res_index: 89
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: B
- chain:
id: C

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example/antibody_scaffolds/nirsevimab.5udc.cif Normal file
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example/antibody_scaffolds/nirsevimab.5udc.yaml Normal file
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# nirsevimab 5udc
# Target: Respiratory Syncytial Virus
# Heavy chain (label not auth): A
# Light chain (label not auth): B
# Full heavy chain sequence: QVQLVQSGAEVKKPGSSVMVSCQASGGLLEDYIINWVRQAPGQGPEWMGGIIPVLGTVHYGPKFQGRVTITADESTDTAYMELSSLRSEDTAMYYCATETALVVSETYLPHYFDNWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS
# Full light chain sequence: DIQMTQSPSSLSAAVGDRVTITCQASQDIVNYLNWYQQKPGKAPKLLIYVASNLETGVPSRFSGSGSGTDFSLTISSLQPEDVATYYCQQYDNLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
# Variable heavy region: 1 - 126
# Variable light region: 1 - 107
# Heavy CDRs: GGLLEDY IPVLGT ETALVVSETYLPHYFDN
# Light CDRs: QASQDIVNYLN VASNLET QQYDNLPLT
#
path: nirsevimab.5udc.cif
include:
- chain:
id: A # heavy
res_index: 1..126
- chain:
id: B # light
res_index: 1..107
design:
- chain:
id: A
res_index: 26..32,52..57,99..115
- chain:
id: B
res_index: 24..34,50..56,89..97
structure_groups:
- group:
id: A
res_index: 26..32,52..57,99..115
visibility: 0
- group:
id: B
res_index: 24..34,50..56,89..97
visibility: 0
exclude:
- chain:
id: A
res_index: 26..32
- chain:
id: A
res_index: 52..57
- chain:
id: A
res_index: 99..115
- chain:
id: B
res_index: 24..34
- chain:
id: B
res_index: 50..56
- chain:
id: B
res_index: 89..97
design_insertions:
- insertion:
id: A
res_index: 26
num_residues: 7..9
- insertion:
id: A
res_index: 52
num_residues: 5..8
- insertion:
id: A
res_index: 99
num_residues: 3..21
- insertion:
id: B
res_index: 24
num_residues: 10..17
- insertion:
id: B
res_index: 50
num_residues: 7
- insertion:
id: B
res_index: 89
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: A
- chain:
id: B

11916
example/antibody_scaffolds/sarilumab.8iow.cif Normal file
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example/antibody_scaffolds/sarilumab.8iow.yaml Normal file
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# sarilumab 8iow
# Target: IL6R/CD126
# Heavy chain (label not auth): D
# Light chain (label not auth): C
# Full heavy chain sequence: EVQLVESGGGLVQPGRSLRLSCAASRFTFDDYAMHWVRQAPGKGLEWVSGISWNSGRIGYADSVKGRFTISRDNAENSLFLQMNGLRAEDTALYYCAKGRDSFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH
# Full light chain sequence: DIQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYGASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFASYYCQQANSFPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
# Variable heavy region: 1 - 116
# Variable light region: 1 - 107
# Heavy CDRs: RFTFDDY SWNSGR GRDSFDI
# Light CDRs: RASQGISSWLA GASSLES QQANSFPYT
#
path: sarilumab.8iow.cif
include:
- chain:
id: D # heavy
res_index: 1..116
- chain:
id: C # light
res_index: 1..107
design:
- chain:
id: D
res_index: 26..32,52..57,99..105
- chain:
id: C
res_index: 24..34,50..56,89..97
structure_groups:
- group:
id: D
res_index: 26..32,52..57,99..105
visibility: 0
- group:
id: C
res_index: 24..34,50..56,89..97
visibility: 0
exclude:
- chain:
id: D
res_index: 26..32
- chain:
id: D
res_index: 52..57
- chain:
id: D
res_index: 99..105
- chain:
id: C
res_index: 24..34
- chain:
id: C
res_index: 50..56
- chain:
id: C
res_index: 89..97
design_insertions:
- insertion:
id: D
res_index: 26
num_residues: 7..9
- insertion:
id: D
res_index: 52
num_residues: 5..8
- insertion:
id: D
res_index: 99
num_residues: 3..21
- insertion:
id: C
res_index: 24
num_residues: 10..17
- insertion:
id: C
res_index: 50
num_residues: 7
- insertion:
id: C
res_index: 89
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: D
- chain:
id: C

12284
example/antibody_scaffolds/secukinumab.6wio.cif Normal file
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example/antibody_scaffolds/secukinumab.6wio.yaml Normal file
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# secukinumab 6wio
# Target: IL17A
# Heavy chain (label not auth): A
# Light chain (label not auth): B
# Full heavy chain sequence: EVQLVESGGGLVQPGGSLRLSCAASGFTFSNYWMNWVRQAPGKGLEWVAAINQDGSEKYYVGSVKGRFTISRDNAKNSLYLQMNSLRVEDTAVYYCVRDYYDILTDYYIHYWYFDLWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
# Full light chain sequence: EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPCTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC
# Variable heavy region: 1 - 127
# Variable light region: 1 - 108
# Heavy CDRs: GFTFSNY NQDGSE DYYDILTDYYIHYWYFDL
# Light CDRs: RASQSVSSSYLA GASSRAT QQYGSSPCT
#
path: secukinumab.6wio.cif
include:
- chain:
id: A # heavy
res_index: 1..127
- chain:
id: B # light
res_index: 1..108
design:
- chain:
id: A
res_index: 26..32,52..57,99..116
- chain:
id: B
res_index: 24..35,51..57,90..98
structure_groups:
- group:
id: A
res_index: 26..32,52..57,99..116
visibility: 0
- group:
id: B
res_index: 24..35,51..57,90..98
visibility: 0
exclude:
- chain:
id: A
res_index: 26..32
- chain:
id: A
res_index: 52..57
- chain:
id: A
res_index: 99..116
- chain:
id: B
res_index: 24..35
- chain:
id: B
res_index: 51..57
- chain:
id: B
res_index: 90..98
design_insertions:
- insertion:
id: A
res_index: 26
num_residues: 7..9
- insertion:
id: A
res_index: 52
num_residues: 5..8
- insertion:
id: A
res_index: 99
num_residues: 3..21
- insertion:
id: B
res_index: 24
num_residues: 10..17
- insertion:
id: B
res_index: 51
num_residues: 7
- insertion:
id: B
res_index: 90
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: A
- chain:
id: B

11814
example/antibody_scaffolds/tezepelumab.5j13.cif Normal file
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example/antibody_scaffolds/tezepelumab.5j13.yaml Normal file
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# tezepelumab 5j13
# Target: TSLP
# Heavy chain (label not auth): C
# Light chain (label not auth): B
# Full heavy chain sequence: MGILPSPGMPALLSLVSLLSVLLMGCVAETGQMQLVESGGGVVQPGRSLRLSCAASGFTFRTYGMHWVRQAPGKGLEWVAVIWYDGSNKHYADSVKGRFTITRDNSKNTLNLQMNSLRAEDTAVYYCARAPQWELVHEAFDIWGQGTMVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVERKGTKHHHHHH
# Full light chain sequence: MGILPSPGMPALLSLVSLLSVLLMGCVAETGSYVLTQPPSVSVAPGQTARITCGGNNLGSKSVHWYQQKPGQAPVLVVYDDSDRPSWIPERFSGSNSGNTATLTISRGEAGDEADYYCQVWDSSSDHVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
# Variable heavy region: 32 - 153
# Variable light region: 32 - 139
# Heavy CDRs: GFTFRTY WYDGSN APQWELVHEAFDI
# Light CDRs: GGNNLGSKSVH DDSDRPS QVWDSSSDHVV
#
path: tezepelumab.5j13.cif
include:
- chain:
id: C # heavy
res_index: 32..153
- chain:
id: B # light
res_index: 32..139
design:
- chain:
id: C
res_index: 57..63,83..88,130..142
- chain:
id: B
res_index: 54..64,80..86,119..129
structure_groups:
- group:
id: C
res_index: 57..63,83..88,130..142
visibility: 0
- group:
id: B
res_index: 54..64,80..86,119..129
visibility: 0
exclude:
- chain:
id: C
res_index: 57..63
- chain:
id: C
res_index: 83..88
- chain:
id: C
res_index: 130..142
- chain:
id: B
res_index: 54..64
- chain:
id: B
res_index: 80..86
- chain:
id: B
res_index: 119..129
design_insertions:
- insertion:
id: C
res_index: 57
num_residues: 7..9
- insertion:
id: C
res_index: 83
num_residues: 5..8
- insertion:
id: C
res_index: 130
num_residues: 3..21
- insertion:
id: B
res_index: 54
num_residues: 10..17
- insertion:
id: B
res_index: 80
num_residues: 7
- insertion:
id: B
res_index: 119
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: C
- chain:
id: B

11937
example/antibody_scaffolds/tralokinumab.5l6y.cif Normal file
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example/antibody_scaffolds/tralokinumab.5l6y.yaml Normal file
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# tralokinumab 5l6y
# Target: IL13
# Heavy chain (label not auth): B
# Light chain (label not auth): C
# Full heavy chain sequence: QVQLVQSGAEVKKPGASVKVSCKASGYTFTNYGLSWVRQAPGQGLEWMGWISANNGDTNYGQEFQGRVTMTTDTSTSTAYMELRSLRSDDTAVYYCARDSSSSWARWFFDLWGRGTLVTVSSASTKGPSVFPLAPISKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVGPSSSLGTQTYICNVNHKPSNTKVDKRVESKYGPPSPSSPAPAKN
# Full light chain sequence: SYVLTQPPSVSVAPGKTARITCGGNIIGSKLVHWYQQKPGQAPVLVIYDDGDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDTGSDPVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
# Variable heavy region: 1 - 122
# Variable light region: 1 - 108
# Heavy CDRs: GYTFTNY SANNGD DSSSSWARWFFDL
# Light CDRs: GGNIIGSKLVH DDGDRPS QVWDTGSDPVV
#
path: tralokinumab.5l6y.cif
include:
- chain:
id: B # heavy
res_index: 1..122
- chain:
id: C # light
res_index: 1..108
design:
- chain:
id: B
res_index: 26..32,52..57,99..111
- chain:
id: C
res_index: 23..33,49..55,88..98
structure_groups:
- group:
id: B
res_index: 26..32,52..57,99..111
visibility: 0
- group:
id: C
res_index: 23..33,49..55,88..98
visibility: 0
exclude:
- chain:
id: B
res_index: 26..32
- chain:
id: B
res_index: 52..57
- chain:
id: B
res_index: 99..111
- chain:
id: C
res_index: 23..33
- chain:
id: C
res_index: 49..55
- chain:
id: C
res_index: 88..98
design_insertions:
- insertion:
id: B
res_index: 26
num_residues: 7..9
- insertion:
id: B
res_index: 52
num_residues: 5..8
- insertion:
id: B
res_index: 99
num_residues: 3..21
- insertion:
id: C
res_index: 23
num_residues: 10..17
- insertion:
id: C
res_index: 49
num_residues: 7
- insertion:
id: C
res_index: 88
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: B
- chain:
id: C

9762
example/antibody_scaffolds/ustekinumab.3hmw.cif Normal file
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example/antibody_scaffolds/ustekinumab.3hmw.yaml Normal file
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# ustekinumab 3hmw
# Target: IL12B/CLMFp40
# Heavy chain (label not auth): B
# Light chain (label not auth): A
# Full heavy chain sequence: EVQLVQSGAEVKKPGESLKISCKGSGYSFTTYWLGWVRQMPGKGLDWIGIMSPVDSDIRYSPSFQGQVTMSVDKSITTAYLQWNSLKASDTAMYYCARRRPGQGYFDFWGQGTLVTVSSSSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH
# Full light chain sequence: DIQMTQSPSSLSASVGDRVTITCRASQGISSWLAWYQQKPEKAPKSLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYNIYPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
# Variable heavy region: 1 - 119
# Variable light region: 1 - 107
# Heavy CDRs: GYSFTTY SPVDSD RRPGQGYFDF
# Light CDRs: RASQGISSWLA AASSLQS QQYNIYPYT
#
path: ustekinumab.3hmw.cif
include:
- chain:
id: B # heavy
res_index: 1..119
- chain:
id: A # light
res_index: 1..107
design:
- chain:
id: B
res_index: 26..32,52..57,99..108
- chain:
id: A
res_index: 24..34,50..56,89..97
structure_groups:
- group:
id: B
res_index: 26..32,52..57,99..108
visibility: 0
- group:
id: A
res_index: 24..34,50..56,89..97
visibility: 0
exclude:
- chain:
id: B
res_index: 26..32
- chain:
id: B
res_index: 52..57
- chain:
id: B
res_index: 99..108
- chain:
id: A
res_index: 24..34
- chain:
id: A
res_index: 50..56
- chain:
id: A
res_index: 89..97
design_insertions:
- insertion:
id: B
res_index: 26
num_residues: 7..9
- insertion:
id: B
res_index: 52
num_residues: 5..8
- insertion:
id: B
res_index: 99
num_residues: 3..21
- insertion:
id: A
res_index: 24
num_residues: 10..17
- insertion:
id: A
res_index: 50
num_residues: 7
- insertion:
id: A
res_index: 89
num_residues: 8..12
# reindex the residue index which is used in the positional encoding
reset_res_index:
- chain:
id: B
- chain:
id: A

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example/antibody_targets/7uxq.cif Normal file
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example/antibody_targets/pdl1.yaml Normal file
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entities:
- file:
include:
- chain:
id: A
path: 7uxq.cif
- file:
path:
- ../antibody_scaffolds/adalimumab.6cr1.yaml
- ../antibody_scaffolds/belimumab.5y9k.yaml
- ../antibody_scaffolds/dupilumab.6wgb.yaml
- ../antibody_scaffolds/golimumab.5yoy.yaml
- ../antibody_scaffolds/guselkumab.4m6m.yaml
- ../antibody_scaffolds/nirsevimab.5udc.yaml
- ../antibody_scaffolds/sarilumab.8iow.yaml
- ../antibody_scaffolds/secukinumab.6wio.yaml
- ../antibody_scaffolds/tezepelumab.5j13.yaml
- ../antibody_scaffolds/tralokinumab.5l6y.yaml
- ../antibody_scaffolds/ustekinumab.3hmw.yaml
- ../antibody_scaffolds/mab1.3h42.yaml
- ../antibody_scaffolds/necitumumab.6b3s.yaml
- ../antibody_scaffolds/crenezumab.5vzy.yaml