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Datasets:
wjulius
/
HumanBindome

Size:
100K<n<1M
Tags:
protein-design
target-binder-design
protein-interface
protein-protein-interaction
structural-biology
benchmark
License:
Dataset card Files
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 Community
6

Add HumanBindome data

#4
by arvban - opened
base: refs/heads/main
←
from: refs/pr/4
Discussion Files changed
+24911
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Files changed (50) hide show
  1. README.md +21 -17
  2. metadata.csv +2 -2
  3. structures/A0/A0A024RBG1.tar +3 -0
  4. structures/A0/A0A024RBG1.tar.gz +0 -3
  5. structures/A0/A0A075B6H7.tar +3 -0
  6. structures/A0/A0A075B6H7.tar.gz +0 -3
  7. structures/A0/A0A075B6H8.tar +3 -0
  8. structures/A0/A0A075B6H8.tar.gz +0 -3
  9. structures/A0/A0A075B6H9.tar +3 -0
  10. structures/A0/A0A075B6H9.tar.gz +0 -3
  11. structures/A0/A0A075B6I0.tar +3 -0
  12. structures/A0/A0A075B6I0.tar.gz +0 -3
  13. structures/A0/A0A075B6I1.tar +3 -0
  14. structures/A0/A0A075B6I1.tar.gz +0 -3
  15. structures/A0/A0A075B6I3.tar +3 -0
  16. structures/A0/A0A075B6I3.tar.gz +0 -3
  17. structures/A0/A0A075B6I4.tar +3 -0
  18. structures/A0/A0A075B6I4.tar.gz +0 -3
  19. structures/A0/A0A075B6I6.tar +3 -0
  20. structures/A0/A0A075B6I6.tar.gz +0 -3
  21. structures/A0/A0A075B6I7.tar +3 -0
  22. structures/A0/A0A075B6I7.tar.gz +0 -3
  23. structures/A0/A0A075B6I9.tar +3 -0
  24. structures/A0/A0A075B6I9.tar.gz +0 -3
  25. structures/A0/A0A075B6J1.tar +3 -0
  26. structures/A0/A0A075B6J1.tar.gz +0 -3
  27. structures/A0/A0A075B6J2.tar +3 -0
  28. structures/A0/A0A075B6J2.tar.gz +0 -3
  29. structures/A0/A0A075B6J6.tar +3 -0
  30. structures/A0/A0A075B6J6.tar.gz +0 -3
  31. structures/A0/A0A075B6J9.tar +3 -0
  32. structures/A0/A0A075B6J9.tar.gz +0 -3
  33. structures/A0/A0A075B6K0.tar +3 -0
  34. structures/A0/A0A075B6K0.tar.gz +0 -3
  35. structures/A0/A0A075B6K2.tar +3 -0
  36. structures/A0/A0A075B6K2.tar.gz +0 -3
  37. structures/A0/A0A075B6K4.tar +3 -0
  38. structures/A0/A0A075B6K4.tar.gz +0 -3
  39. structures/A0/A0A075B6K5.tar +3 -0
  40. structures/A0/A0A075B6K5.tar.gz +0 -3
  41. structures/A0/A0A075B6L2.tar +3 -0
  42. structures/A0/A0A075B6L2.tar.gz +0 -3
  43. structures/A0/A0A075B6L6.tar +3 -0
  44. structures/A0/A0A075B6L6.tar.gz +0 -3
  45. structures/A0/A0A075B6N1.tar +3 -0
  46. structures/A0/A0A075B6N1.tar.gz +0 -3
  47. structures/A0/A0A075B6N2.tar +3 -0
  48. structures/A0/A0A075B6N2.tar.gz +0 -3
  49. structures/A0/A0A075B6N3.tar +3 -0
  50. structures/A0/A0A075B6N3.tar.gz +0 -3
README.md CHANGED
@@ -27,7 +27,7 @@ The dataset is intended for machine-learning studies of designed protein-protein
27
 
28
  The dataset is indexed by a single `metadata.csv` file. Benchmark partitions are encoded in the `split` column. Structure paths are provided directly in the metadata table.
29
 
30
- The released complex structures are full target-binder complex models in a superimposed coordinate frame. The relative path to each structure is given in the `target_binder_complex_pdb_path` column. Predicted apo structures for the target and binder are provided under `target_alone_pdb_path` and `binder_alone_pdb_path`.
31
 
32
  Repository organization:
33
 
@@ -37,19 +37,21 @@ Repository organization:
37
  ├── metadata.csv
38
  └── structures/
39
  ├── [xx]/ # first two characters of target_name
40
- │ ├── [target_name_1].tar.gz
41
- │ └── [target_name_2].tar.gz
42
  └── ...
43
  ```
44
 
45
- Each archive contains the structure files for one target:
46
 
47
  ```text
48
- [target_name].tar.gz
49
- └── [target_domain]/
50
- ├── [design_name].pdb
51
- ├── [design_name]_binder_alone.pdb
52
- └── [design_name]_full_target_structure.pdb
 
 
53
  ```
54
 
55
  ## Metadata Columns
@@ -64,10 +66,12 @@ Each archive contains the structure files for one target:
64
  | `split` | Split assignment: `train`, `validation`, `test`, or `deleaked`. |
65
  | `paired_interface_cluster_id` | Paired target-side/binder-side interface cluster identifier used for leakage-controlled splitting. |
66
  | `cluster_member_type` | Cluster membership annotation for the validation and test splits. `cluster_rep` denotes the randomly selected representative used for one-per-cluster validation/test evaluation; `cluster_member` denotes other members of the same cluster. |
67
- | `structure_archive` | Relative path to the target-level `tar.gz` archive containing the structure files. |
68
  | `target_binder_complex_pdb_path` | Path inside the archive to the superimposed target-domain–binder complex PDB file. |
69
  | `binder_alone_pdb_path` | Path inside the archive to the binder-only PDB file. |
70
- | `target_alone_pdb_path` | Path inside the archive to the target-only PDB file. |
 
 
71
 
72
  ## Dataset Splits
73
 
@@ -75,12 +79,12 @@ The dataset provides predefined train, validation, and test partitions. Complexe
75
 
76
  | Split | Complexes | Share |
77
  |---|---:|---:|
78
- | train | 131,939 | 43.10% |
79
- | validation | 53,549 | 17.49% |
80
- | test | 52,137 | 17.03% |
81
  | deleaked | 68,521 | 22.38% |
82
- | total | 306,146 | 100.00% |
83
- | usable benchmark | 237,625 | 77.62% |
84
 
85
  The usable benchmark consists of the train, validation, and test partitions only.
86
 
@@ -102,7 +106,7 @@ As an independent audit, we assessed whether ProteinMPNN sister variants derived
102
 
103
  Among 120,609 backbones with ProteinMPNN sister variants, 120,082 were contained within a single paired-interface cluster, whereas 527 were split across multiple clusters. 99.56% of multi-member backbone groups were captured by the paired-interface clustering procedure.
104
 
105
- After deleaking, only 14 of the 85,037 multi-member backbone groups in the usable benchmark (0.016%) have sister variants split between `train` and the held-out (`validation` or `test`) split.
106
 
107
 
108
  ## Intended Use
 
27
 
28
  The dataset is indexed by a single `metadata.csv` file. Benchmark partitions are encoded in the `split` column. Structure paths are provided directly in the metadata table.
29
 
30
+ The released complex structures are full target-binder complex models in a superimposed coordinate frame. The relative path to each structure is given in the `target_binder_complex_pdb_path` column. Predicted apo structures for the target domain and binder are provided under `target_domain_pdb_path` and `binder_alone_pdb_path`, and the full-length apo target structure under `target_structure_pdb_path`.
31
 
32
  Repository organization:
33
 
 
37
  ├── metadata.csv
38
  └── structures/
39
  ├── [xx]/ # first two characters of target_name
40
+ │ ├── [target_name_1].tar
41
+ │ └── [target_name_2].tar
42
  └── ...
43
  ```
44
 
45
+ Each archive is an uncompressed `.tar` containing the structure files for one target:
46
 
47
  ```text
48
+ [target_name].tar
49
+ ├── [target_name].pdb # full-length predicted target structure
50
+ └── [target_name]_[domain]/
51
+ ├── [target_name]_[domain].pdb # predicted apo target domain
52
+ └── [design_name]/
53
+ ├── [design_name].pdb # superimposed target-binder complex
54
+ └── [design_name]_binder_alone.pdb # predicted apo binder
55
  ```
56
 
57
  ## Metadata Columns
 
66
  | `split` | Split assignment: `train`, `validation`, `test`, or `deleaked`. |
67
  | `paired_interface_cluster_id` | Paired target-side/binder-side interface cluster identifier used for leakage-controlled splitting. |
68
  | `cluster_member_type` | Cluster membership annotation for the validation and test splits. `cluster_rep` denotes the randomly selected representative used for one-per-cluster validation/test evaluation; `cluster_member` denotes other members of the same cluster. |
69
+ | `structure_archive` | Relative path to the target-level `tar` archive containing the structure files. |
70
  | `target_binder_complex_pdb_path` | Path inside the archive to the superimposed target-domain–binder complex PDB file. |
71
  | `binder_alone_pdb_path` | Path inside the archive to the binder-only PDB file. |
72
+ | `target_domain_pdb_path` | Path inside the archive to the apo target-domain PDB file (one per target domain, shared across its designs). |
73
+ | `target_structure_pdb_path` | Path inside the archive to the full-length apo target structure PDB file (one per target). |
74
+ | `binder_sequence` | Amino-acid sequence (one-letter) of the designed binder, parsed from the apo binder PDB. |
75
 
76
  ## Dataset Splits
77
 
 
79
 
80
  | Split | Complexes | Share |
81
  |---|---:|---:|
82
+ | train | 131,936 | 43.10% |
83
+ | validation | 53,548 | 17.49% |
84
+ | test | 52,132 | 17.03% |
85
  | deleaked | 68,521 | 22.38% |
86
+ | total | 306,137 | 100.00% |
87
+ | usable benchmark | 237,616 | 77.62% |
88
 
89
  The usable benchmark consists of the train, validation, and test partitions only.
90
 
 
106
 
107
  Among 120,609 backbones with ProteinMPNN sister variants, 120,082 were contained within a single paired-interface cluster, whereas 527 were split across multiple clusters. 99.56% of multi-member backbone groups were captured by the paired-interface clustering procedure.
108
 
109
+ After deleaking, only 14 of the 85,036 multi-member backbone groups in the usable benchmark (0.016%) have sister variants split between `train` and the held-out (`validation` or `test`) split.
110
 
111
 
112
  ## Intended Use
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