BioLiP

To facilitate template-based protein-ligand docking and protein function annotation, all data from the BioLiP database are freely available. You can download them from the links provided below.

BioLiP raw data
Download structures for protein-ligand interactions.
Download ligand summary (see readme_ligand.txt for explanation).
Download redundant dataset

Link	Description
BioLiP.txt.gz	Annotations for each ligand-protein interaction site (readme)
protein.fasta.gz	Protein receptor sequences
dna.fasta.gz	DNA ligand sequences
rna.fasta.gz	RNA ligand sequences
peptide.fasta.gz	Peptide ligand sequences

In January 2025, 24809 affinity data from PDBbind-CN are removed due to licensing issue.

Download non-redundant dataset

Link	Description
BioLiP_nr.txt.gz	Annotations for each ligand-protein interaction site (readme)
protein_nr.fasta.gz	Protein receptor sequences clustered with 90% identity cutoff
dna_nr.fasta.gz	DNA ligand sequences clustered with 100% identity cutoff
rna_nr.fasta.gz	RNA ligand sequences clustered with 100% identity cutoff
peptide_nr.fasta.gz	Peptide ligand sequences clustered with 100% identity cutoff

All sequences are converted from residues with experimentally determined coordinates in the structure; residues unobserved in the structure are excluded.

BioLiP source code
Download the source code for BioLiP database curation and web interface display

Template library for protein function prediction by COACH and COFACTOR
Download the library

Standalone package for protein function prediction by COACH and COFACTOR
Donwload through the I-TASSER Suite

Reference:
Jianyi Yang, Ambrish Roy, and Yang Zhang. BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions, Nucleic Acids Research, 41: D1096-D1103 (2013) (download the PDF file).