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Add antibody-antigen metadata from AlphaFold 3 paper

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PiperOrigin-RevId: 717534278
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Augustin Zidek
2025-01-20 17:21:34 +00:00
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pdb_id,chain_id_1,chain_id_2,cluster_key_chain_1,cluster_key_chain_2,interface_cluster_key
7fci,A,B,5581,5964,5581|5964
7fci,A,C,5581,17640,17640|5581
7mnl,A,C,8677,17640,17640|8677
7n0a,A,B,33602,5964,33602|5964
7n0a,A,C,33602,17640,17640|33602
7ox1,A,G,17640,41184,17640|41184
7ox1,B,G,5964,41184,41184|5964
7ox2,A,C,17640,41184,17640|41184
7ox2,B,C,5964,41184,41184|5964
7ox3,A,C,5964,41184,41184|5964
7ox3,B,C,17640,41184,17640|41184
7ox4,A,C,17640,41184,17640|41184
7ox4,B,C,5964,41184,41184|5964
7q6c,A,B,15496,17640,15496|17640
7q6c,A,D,15496,5964,15496|5964
7r58,A,B,30790,17640,17640|30790
7r58,A,C,30790,5964,30790|5964
7ru6,A,B,7068,17640,17640|7068
7sbd,A,C,17640,20692,17640|20692
7sbd,B,C,5964,20692,20692|5964
7sbg,A,C,17640,20692,17640|20692
7sbg,B,C,5964,20692,20692|5964
7sjo,A,F,7390,17640,17640|7390
7sjo,A,I,7390,5964,5964|7390
7sjo,B,G,7390,17640,17640|7390
7sjo,B,H,7390,5964,5964|7390
7sjo,C,D,7390,17640,17640|7390
7sjo,C,E,7390,5964,5964|7390
7sk3,A,C,45640,5964,45640|5964
7sk3,A,D,45640,17640,17640|45640
7sk3,A,E,45640,5964,45640|5964
7sk3,A,F,45640,17640,17640|45640
7sk4,A,C,45640,5964,45640|5964
7sk4,A,D,45640,17640,17640|45640
7sk4,A,E,45640,5964,45640|5964
7sk4,A,F,45640,17640,17640|45640
7sk5,A,B,45640,17640,17640|45640
7sk5,A,D,45640,5964,45640|5964
7sk6,A,C,45640,5964,45640|5964
7sk6,A,D,45640,17640,17640|45640
7sk7,A,C,45640,5964,45640|5964
7sk7,A,D,45640,17640,17640|45640
7sk8,A,C,45640,5964,45640|5964
7sk8,A,D,45640,17640,17640|45640
7sk8,A,E,45640,5964,45640|5964
7sk8,A,F,45640,17640,17640|45640
7sk9,A,B,45640,17640,17640|45640
7sk9,A,C,45640,5964,45640|5964
7st8,A,C,17640,41188,17640|41188
7st8,B,C,5964,41188,41188|5964
7t6x,E,H,5964,24273,24273|5964
7t82,A,C,9703,5964,5964|9703
7t82,A,D,9703,17640,17640|9703
7t9m,A,C,17640,13210,13210|17640
7t9m,B,C,5964,13210,13210|5964
7t9n,A,D,5964,13210,13210|5964
7t9n,B,D,17640,13210,13210|17640
7tuf,A,B,22549,17640,17640|22549
7tuf,A,C,22549,5964,22549|5964
7tuf,A,E,22549,17640,17640|22549
7tuf,B,D,17640,22549,17640|22549
7tuf,D,E,22549,17640,17640|22549
7tuf,D,F,22549,5964,22549|5964
7tug,A,B,22549,17640,17640|22549
7tug,A,C,22549,5964,22549|5964
7u8c,A,B,20081,17640,17640|20081
7u8c,A,C,20081,5964,20081|5964
7u8g,A,C,29632,17640,17640|29632
7u8g,A,D,29632,5964,29632|5964
7uih,A,B,11223,5964,11223|5964
7uih,A,C,11223,17640,11223|17640
7uih,A,D,11223,5964,11223|5964
7uih,A,E,11223,17640,11223|17640
7um3,A,E,17640,33649,17640|33649
7um3,B,E,5964,33649,33649|5964
7ura,A,B,44530,5964,44530|5964
7ura,A,C,44530,17640,17640|44530
7urc,A,B,44530,5964,44530|5964
7urc,A,C,44530,17640,17640|44530
7urd,A,C,44530,5964,44530|5964
7urd,A,D,44530,17640,17640|44530
7ure,A,B,44530,5964,44530|5964
7ure,A,C,44530,17640,17640|44530
7uvf,A,C,23558,17640,17640|23558
7uvf,A,D,23558,5964,23558|5964
7uvf,B,E,23558,5964,23558|5964
7uvf,B,F,23558,17640,17640|23558
7vad,A,B,5581,17640,17640|5581
7vad,A,C,5581,5964,5581|5964
7vae,A,B,5581,17640,17640|5581
7vae,A,C,5581,5964,5581|5964
7vaf,A,C,17640,5581,17640|5581
7vaf,B,C,5964,5581,5581|5964
7vag,A,B,5581,17640,17640|5581
7vag,A,C,5581,5964,5581|5964
7vgr,A,E,5964,33673,33673|5964
7vgr,A,F,5964,33673,33673|5964
7vgr,B,E,17640,33673,17640|33673
7vgr,B,F,17640,33673,17640|33673
7vgr,C,E,5964,33673,33673|5964
7vgr,C,F,5964,33673,33673|5964
7vgr,D,E,17640,33673,17640|33673
7vgr,D,F,17640,33673,17640|33673
7vgs,A,B,33673,5964,33673|5964
7vgs,A,C,33673,17640,17640|33673
7vgs,A,E,33673,5964,33673|5964
7vgs,B,D,5964,33673,33673|5964
7vgs,D,E,33673,5964,33673|5964
7vgs,D,F,33673,17640,17640|33673
7vn9,A,C,17640,20046,17640|20046
7vn9,B,C,5964,20046,20046|5964
7vng,A,B,20046,17640,17640|20046
7vng,A,C,20046,5964,20046|5964
7w71,A,E,24335,17640,17640|24335
7w71,A,F,24335,5964,24335|5964
7wsi,A,B,5581,17640,17640|5581
7wsi,A,C,5581,5964,5581|5964
7xq8,A,B,26372,5964,26372|5964
7xq8,C,D,26372,5964,26372|5964
7zlg,A,D,17640,29547,17640|29547
7zlg,C,D,5964,29547,29547|5964
7zlh,A,D,17640,29547,17640|29547
7zlh,C,D,5964,29547,29547|5964
7zli,A,D,17640,29547,17640|29547
7zli,C,D,5964,29547,29547|5964
7zlj,A,D,17640,29547,17640|29547
7zlj,C,D,5964,29547,29547|5964
7zwi,A,C,7003,5964,5964|7003
7zxf,A,C,7003,5964,5964|7003
7zxf,A,E,7003,5964,5964|7003
7zxg,A,C,7003,5964,5964|7003
7zxk,A,F,26707,5964,26707|5964
7zxk,A,G,26707,17640,17640|26707
7zyi,A,B,5581,17640,17640|5581
7zyi,A,C,5581,5964,5581|5964
8cz5,A,B,24059,17640,17640|24059
8cz5,A,C,24059,5964,24059|5964
8dcy,A,C,17640,23342,17640|23342
8dcy,B,C,5964,23342,23342|5964
8ddk,A,C,17640,23342,17640|23342
8ddk,B,C,5964,23342,23342|5964
8djk,A,E,15456,17640,15456|17640
8djk,B,D,15455,5964,15455|5964
8djk,B,E,15455,17640,15455|17640
8djm,A,E,15456,17640,15456|17640
8djm,B,D,15455,5964,15455|5964
8djm,B,E,15455,17640,15455|17640
8dke,A,B,13979,17640,13979|17640
8dke,A,C,13979,5964,13979|5964
8dki,A,B,13979,17640,13979|17640
8dki,A,C,13979,5964,13979|5964
8dkm,A,C,17640,13979,13979|17640
8dkm,B,C,5964,13979,13979|5964
8dkw,A,C,17640,13979,13979|17640
8dkw,B,C,5964,13979,13979|5964
8dkx,A,C,17640,13979,13979|17640
8dkx,B,C,5964,13979,13979|5964
8hii,A,B,21158,17640,17640|21158
8hii,A,D,21158,5964,21158|5964
8hij,A,B,21158,17640,17640|21158
8hij,A,D,21158,5964,21158|5964
8hik,A,B,21158,17640,17640|21158
8hik,A,D,21158,5964,21158|5964
7so7,A,F,3006,5964,3006|5964
7xy8,A,C,2517,17640,17640|2517
7xy8,A,E,2517,5964,2517|5964
1 pdb_id chain_id_1 chain_id_2 cluster_key_chain_1 cluster_key_chain_2 interface_cluster_key
2 7fci A B 5581 5964 5581|5964
3 7fci A C 5581 17640 17640|5581
4 7mnl A C 8677 17640 17640|8677
5 7n0a A B 33602 5964 33602|5964
6 7n0a A C 33602 17640 17640|33602
7 7ox1 A G 17640 41184 17640|41184
8 7ox1 B G 5964 41184 41184|5964
9 7ox2 A C 17640 41184 17640|41184
10 7ox2 B C 5964 41184 41184|5964
11 7ox3 A C 5964 41184 41184|5964
12 7ox3 B C 17640 41184 17640|41184
13 7ox4 A C 17640 41184 17640|41184
14 7ox4 B C 5964 41184 41184|5964
15 7q6c A B 15496 17640 15496|17640
16 7q6c A D 15496 5964 15496|5964
17 7r58 A B 30790 17640 17640|30790
18 7r58 A C 30790 5964 30790|5964
19 7ru6 A B 7068 17640 17640|7068
20 7sbd A C 17640 20692 17640|20692
21 7sbd B C 5964 20692 20692|5964
22 7sbg A C 17640 20692 17640|20692
23 7sbg B C 5964 20692 20692|5964
24 7sjo A F 7390 17640 17640|7390
25 7sjo A I 7390 5964 5964|7390
26 7sjo B G 7390 17640 17640|7390
27 7sjo B H 7390 5964 5964|7390
28 7sjo C D 7390 17640 17640|7390
29 7sjo C E 7390 5964 5964|7390
30 7sk3 A C 45640 5964 45640|5964
31 7sk3 A D 45640 17640 17640|45640
32 7sk3 A E 45640 5964 45640|5964
33 7sk3 A F 45640 17640 17640|45640
34 7sk4 A C 45640 5964 45640|5964
35 7sk4 A D 45640 17640 17640|45640
36 7sk4 A E 45640 5964 45640|5964
37 7sk4 A F 45640 17640 17640|45640
38 7sk5 A B 45640 17640 17640|45640
39 7sk5 A D 45640 5964 45640|5964
40 7sk6 A C 45640 5964 45640|5964
41 7sk6 A D 45640 17640 17640|45640
42 7sk7 A C 45640 5964 45640|5964
43 7sk7 A D 45640 17640 17640|45640
44 7sk8 A C 45640 5964 45640|5964
45 7sk8 A D 45640 17640 17640|45640
46 7sk8 A E 45640 5964 45640|5964
47 7sk8 A F 45640 17640 17640|45640
48 7sk9 A B 45640 17640 17640|45640
49 7sk9 A C 45640 5964 45640|5964
50 7st8 A C 17640 41188 17640|41188
51 7st8 B C 5964 41188 41188|5964
52 7t6x E H 5964 24273 24273|5964
53 7t82 A C 9703 5964 5964|9703
54 7t82 A D 9703 17640 17640|9703
55 7t9m A C 17640 13210 13210|17640
56 7t9m B C 5964 13210 13210|5964
57 7t9n A D 5964 13210 13210|5964
58 7t9n B D 17640 13210 13210|17640
59 7tuf A B 22549 17640 17640|22549
60 7tuf A C 22549 5964 22549|5964
61 7tuf A E 22549 17640 17640|22549
62 7tuf B D 17640 22549 17640|22549
63 7tuf D E 22549 17640 17640|22549
64 7tuf D F 22549 5964 22549|5964
65 7tug A B 22549 17640 17640|22549
66 7tug A C 22549 5964 22549|5964
67 7u8c A B 20081 17640 17640|20081
68 7u8c A C 20081 5964 20081|5964
69 7u8g A C 29632 17640 17640|29632
70 7u8g A D 29632 5964 29632|5964
71 7uih A B 11223 5964 11223|5964
72 7uih A C 11223 17640 11223|17640
73 7uih A D 11223 5964 11223|5964
74 7uih A E 11223 17640 11223|17640
75 7um3 A E 17640 33649 17640|33649
76 7um3 B E 5964 33649 33649|5964
77 7ura A B 44530 5964 44530|5964
78 7ura A C 44530 17640 17640|44530
79 7urc A B 44530 5964 44530|5964
80 7urc A C 44530 17640 17640|44530
81 7urd A C 44530 5964 44530|5964
82 7urd A D 44530 17640 17640|44530
83 7ure A B 44530 5964 44530|5964
84 7ure A C 44530 17640 17640|44530
85 7uvf A C 23558 17640 17640|23558
86 7uvf A D 23558 5964 23558|5964
87 7uvf B E 23558 5964 23558|5964
88 7uvf B F 23558 17640 17640|23558
89 7vad A B 5581 17640 17640|5581
90 7vad A C 5581 5964 5581|5964
91 7vae A B 5581 17640 17640|5581
92 7vae A C 5581 5964 5581|5964
93 7vaf A C 17640 5581 17640|5581
94 7vaf B C 5964 5581 5581|5964
95 7vag A B 5581 17640 17640|5581
96 7vag A C 5581 5964 5581|5964
97 7vgr A E 5964 33673 33673|5964
98 7vgr A F 5964 33673 33673|5964
99 7vgr B E 17640 33673 17640|33673
100 7vgr B F 17640 33673 17640|33673
101 7vgr C E 5964 33673 33673|5964
102 7vgr C F 5964 33673 33673|5964
103 7vgr D E 17640 33673 17640|33673
104 7vgr D F 17640 33673 17640|33673
105 7vgs A B 33673 5964 33673|5964
106 7vgs A C 33673 17640 17640|33673
107 7vgs A E 33673 5964 33673|5964
108 7vgs B D 5964 33673 33673|5964
109 7vgs D E 33673 5964 33673|5964
110 7vgs D F 33673 17640 17640|33673
111 7vn9 A C 17640 20046 17640|20046
112 7vn9 B C 5964 20046 20046|5964
113 7vng A B 20046 17640 17640|20046
114 7vng A C 20046 5964 20046|5964
115 7w71 A E 24335 17640 17640|24335
116 7w71 A F 24335 5964 24335|5964
117 7wsi A B 5581 17640 17640|5581
118 7wsi A C 5581 5964 5581|5964
119 7xq8 A B 26372 5964 26372|5964
120 7xq8 C D 26372 5964 26372|5964
121 7zlg A D 17640 29547 17640|29547
122 7zlg C D 5964 29547 29547|5964
123 7zlh A D 17640 29547 17640|29547
124 7zlh C D 5964 29547 29547|5964
125 7zli A D 17640 29547 17640|29547
126 7zli C D 5964 29547 29547|5964
127 7zlj A D 17640 29547 17640|29547
128 7zlj C D 5964 29547 29547|5964
129 7zwi A C 7003 5964 5964|7003
130 7zxf A C 7003 5964 5964|7003
131 7zxf A E 7003 5964 5964|7003
132 7zxg A C 7003 5964 5964|7003
133 7zxk A F 26707 5964 26707|5964
134 7zxk A G 26707 17640 17640|26707
135 7zyi A B 5581 17640 17640|5581
136 7zyi A C 5581 5964 5581|5964
137 8cz5 A B 24059 17640 17640|24059
138 8cz5 A C 24059 5964 24059|5964
139 8dcy A C 17640 23342 17640|23342
140 8dcy B C 5964 23342 23342|5964
141 8ddk A C 17640 23342 17640|23342
142 8ddk B C 5964 23342 23342|5964
143 8djk A E 15456 17640 15456|17640
144 8djk B D 15455 5964 15455|5964
145 8djk B E 15455 17640 15455|17640
146 8djm A E 15456 17640 15456|17640
147 8djm B D 15455 5964 15455|5964
148 8djm B E 15455 17640 15455|17640
149 8dke A B 13979 17640 13979|17640
150 8dke A C 13979 5964 13979|5964
151 8dki A B 13979 17640 13979|17640
152 8dki A C 13979 5964 13979|5964
153 8dkm A C 17640 13979 13979|17640
154 8dkm B C 5964 13979 13979|5964
155 8dkw A C 17640 13979 13979|17640
156 8dkw B C 5964 13979 13979|5964
157 8dkx A C 17640 13979 13979|17640
158 8dkx B C 5964 13979 13979|5964
159 8hii A B 21158 17640 17640|21158
160 8hii A D 21158 5964 21158|5964
161 8hij A B 21158 17640 17640|21158
162 8hij A D 21158 5964 21158|5964
163 8hik A B 21158 17640 17640|21158
164 8hik A D 21158 5964 21158|5964
165 7so7 A F 3006 5964 3006|5964
166 7xy8 A C 2517 17640 17640|2517
167 7xy8 A E 2517 5964 2517|5964

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# Metadata for Antibody-Antigen pairs used to create figure 5a.
Figure 5a in the AlphaFold 3 paper was created using 71 antibody–antigen
complexes, containing 166 antibody–antigen interfaces spanning 65 interface
clusters. Scores were averaged within each interface cluster then across
clusters. We provide metadata for these complexes and the associated clusters in
this CSV file:
https://github.com/google-deepmind/alphafold3/blob/main/docs/metadata_antibody_antigen.csv