BioLiP is a semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions. The structure data are collected primarily from the Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. BioLiP aims to construct the most comprehensive and accurate database for serving the needs of ligand-protein docking, virtual ligand screening and protein function annotation. Questions about the BioLiP Database can be posted at the Service System Discussion Board.

Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as additives (i.e., false positives) for solving the protein structures, not all ligands present in the PDB database are biologically relevant. BioLiP uses a composite automated and manual procedure for examining the biological relevance of ligands in the PDB database. Each entry in BioLiP contains a comprehensive list of annotations on:

ligand-binding residues;

ligand binding affinity (from the original literature, plus Binding MOAD, PDBbind-CN, BindingDB);

catalytic site residues (mapped from Mechanism and Catalytic Site Atlas);

Enzyme Commission (EC) numbers and Gene Ontology (GO) terms mapped by the SIFTS database;

crosslinks to external databases, including RCSB PDB, PDBe, PDBj, PDBsum, Binding MOAD, PDBbind-CN, Mechanism and Catalytic Site Atlas, QuickGO, ExPASy ENZYME, ChEMBL, DrugBank, ZINC, UniProt, PubMed.

In Feburary 2023, BioLiP was updated to BioLiP2, where newly added features are explained here.

BioLiP in numbers

BioLiP is updated weekly and the current version (2024-09-28) contains:

Number of entries: 903398

Number of entries for regular ligands: 460725

Number of entries for metal ligands: 197122

Number of entries for peptide ligands: 39065

Number of entries for DNA ligands: 45686

Number of entries for RNA ligands: 160800

Number of entries with binding affinity data: 903398 (26009 from Binding MOAD, 24809 from PDBbind-CN, 19354 from BindingDB, and 81 from manual survey of the original literature)

Number of protein receptors: 467139

Number of protein receptors with Enzyme Commission numbers: 431294

Number of protein receptors with Gene Ontology annotations: 418164 (395560 with Molecular Function, 363304 with Biological Process, and 302160 with Cellular Component)

View an example BioLiP entry

Search BioLiP by name

PDB ID
PDB Chain ID
Ligand ID
UniProt accession
EC number
GO term
Ligand name
PubMed ID
With binding affinity data	Check this box to restrict search to entries with binding affinity from MOAD, PDBbind-CN, BindingDB, or manual survey of original literature.

  

Search BioLiP by sequence

Paste your sequence here:     [Sample protein input] [Sample peptide input] [Sample rna input] [Sample dna input]

Select Sequence type:     Protein receptor     Peptide ligand     RNA ligand     DNA ligand
  

Search BioLiP by protein structure

Paste your structure here:     [Sample PDB ID] [Sample UniProt accession] [Sample PDB file]

Or upload PDB or mmCIF format structure file from your computer: