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BioLiP
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.
  • Search BioLiP by sequence

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

    Or upload sequence from your computer:
    Select Sequence type:     Protein receptor     Peptide ligand     RNA ligand     DNA ligand
      

    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.
      


    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).

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