PDB
Datasets
All datasets matching “PDB”PDBbind_testPDBbindPDB
PDB mmCIF Entry Index
The Protein Data Bank is the single global archive of experimentally-determined 3D structures of biological macromolecules, established in 1971 and now holding well over 230,000 entries. It stores atomic coordinates for proteins, nucleic acids, and their complexes determined by X-ray crystallography, cryo-EM, NMR, micro-electron diffraction, and integrative methods, along with the underlying experimental data (structure factors, EM maps, NMR restraints) and… See the full description on the dataset page: https://huggingface.co/datasets/LiteFold/PDB.PDB
Data types
sequence: 355 datapoints
structure: 355 datapoints
pdb-dbpdb_protein_ligand_complexes
How to use the data sets
This dataset contains about 36,000 unique pairs of protein sequences and ligand SMILES, and the coordinates
of their complexes from the PDB.
SMILES are assumed to be tokenized by the regex from P. Schwaller.
Ligand selection criteria
Only ligands
that have at least 3 atoms,
a molecular weight >= 100 Da,
and which are not among the 280 most common ligands in the PDB (this includes common additives like PEG, ADP, ..)
are considered.
Use… See the full description on the dataset page: https://huggingface.co/datasets/jglaser/pdb_protein_ligand_complexes.