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,
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,
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 (2025年07月30日) contains:
Number of entries: 989724
Number of entries for regular ligands: 501072
Number of entries for metal ligands: 213844
Number of entries for peptide ligands: 41570
Number of entries for DNA ligands: 50999
Number of entries for RNA ligands: 182239
Number of entries with binding affinity data: 989724
(25999 from Binding MOAD,
19352 from BindingDB, and
81 from manual survey of the original literature)
Number of protein receptors: 512101
Number of protein receptors with Enzyme Commission numbers: 431124
Number of protein receptors with Gene Ontology annotations: 434445
(410081 with Molecular Function,
376887 with Biological Process, and
315637 with Cellular Component)
Search BioLiP by name
Search BioLiP by sequence
Search BioLiP by protein structure
Reference:
-
Chengxin Zhang, Xi Zhang, Peter L Freddolino, and Yang Zhang.
BioLiP2: an updated structure database for biologically relevent ligand-protein interactions, Nucleic Acids Research, gkad630 (2023)(download the PDF file).
-
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).