Table 1A.
The ligand pocket benchmark dataset from Kahraman et al.
| Binding ligand molecule | Number of PDB entries | PDB entries |
|---|---|---|
| AMP | 9 | 12asA, 1amuA, 1c0aA, 1ct9A, 1jp4A, 1khtB, 1qb8A, 1tb7B, 8gpbA |
| ATP | 14 | 1a0iA, 1a49A, 1aylA, 1b8aA, 1dv2A, 1dy3A, 1e2qA, 1e8xA, 1esqA, 1gn8B, 1kvkA, 1o9tA, 1rdqE, 1tidA |
| FAD | 10 | 1cqxA, 1e8gB, 1eviB, 1h69A, 1hskA, 1jqiA, 1jr8B, 1k87A, 1poxA, 3grsA |
| FMN | 6 | 1dnlA, 1f6vA, 1ja1A, 1mvlA, 1p4cA, 1p4mA |
| GLC | 5 | 1bdgA, 1cq1A, 1k1wA, 1nf5C, 2gbpA |
| HEM | 16 | 1d0cA, 1d7cA, 1dk0A, 1eqgA, 1ew0A, 1gweA, 1iqcA, 1nazE, 1np4B, 1po5A, 1pp9C, 1qhuA, 1qlaC, 1qpaB, 1soxA, 2cpoA |
| NAD | 15 | 1ej2B, 1hexA, 1ib0A, 1jq5A, 1mewA, 1mi3A, 1o04A, 1og3A, 1qaxA, 1rlzA, 1s7gB, 1t2dA, 1toxA, 2a5fB, 2npxA |
| PO4 | 20 | 1a6q, 1b8oC, 1brwA, 1cqjB, 1d1qB, 1dakA, 1e9gA, 1ejdC, 1eucA, 1ew2A, 1fbtB, 1gypA, 1h6lA, 1ho5B, 1l5wA, 1l7mA, 1lbyA, 1lyvA, 1qf5A, 1tcoA |
| STR | 5 | 1e3rB, 1fdsA, 1j99A, 1lhuA, 1qktA |
The list of the proteins are compiled by Kahraman et al.55 and shown as Table 1 in their paper with detailed information of the proteins. Here only PDB IDs are provided for readers’ convenience. Underlined entries in Tables 1A and 1B are used in the performance comparison with eF-Seek and SiteBase, as these are commonly included in the database of the two methods. The entries with double underline are used as queries.