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Table 1 The databases of ligand-receptor pairs

From: Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level

Database Ligand-receptor complexs Level Species Pairs number Verified Address Author
The database of interacting proteins (DIP) [18, 19] Yes Protein Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Drosophila melanogaster, Escherichia coli, Caenorhabditis elegans, Helicobacter pylori, Bos taurus, Arabidopsis thaliana 81,923 Yes http://dip.doe-mbi.ucla.edu Lukasz Salwinski et al.
Database of ligand-receptor partners (DLRP) [20] No Protein NA NA Yes NA Graeber et al.
Human plasma membrane receptome (HPMR) database [21] No Protein Homo sapiens NA Yes http://Receptome.Stanford.edu Izhar Ben-Shlomo et al.
The Online Predicted Human Interaction Database (OPHID) [22] Yes Protein Homo sapiens,Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Mus musculus 23,889 Part http: //ophid.utoronto.ca Kevin R Brown et al.
Mother Of All Databases (Binding MOAD) [23] Yes Protein NA 38,702 Yes http://www.BindingMOAD.org Liegi Hu et al.
Unified Human Interactome database (UniHI) [24] No Protein Homo sapiens 150,000 Part http://www.mdc-berlin.de/unihi Gautam Chaurasia et al.
Interolog interaction database (I2D) [25] No Protein Homo sapiens,Saccharomyces cerevisiae, Caenorhabditis elegans, Rattus norvegicus, Drosophila melanogaster and Mus musculus 1,279,157 Part http://ophid.utoronto.ca/i2d/ Kevin R Brown et al.
GPCR-Ligand Database (GLIDA) [26] Yes Protein NA 39,140 Yes http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ Yasushi Okuno et al.
ConsensusPathDB [27,28,29] No Protein and gene Homo sapiens 215 541 Part http://ConsensusPathDB.org Atanas Kamburov et al.
The International Union of Basic and Clinical Pharmacology database (IUPHAR-DB) [30, 31] Yes Protein and gene Homo sapiens 48,902 Part http://www.iuphar-db.org Sharman et al.
The molecular interaction database (MINT) [32] No Protein NA 235,000 Part http://mint.bio.uniroma2.it/mint/ Luana Licata et al.
InnateDB [33] No Protein and gene Homo sapiens, Mus musculus and Bos taurus 18,780 Yes http://www.innatedb.com Karin Breuer et al.
The STRING database [34, 35] No Protein 5090 organisms 3,123,056,667 Part http://string-db.org/ Izhar Ben-Shlomo et al.
The TissueNet database [36] No Protein Homo sapiens NA Part http://netbio.bgu.ac.il/tissuenet/ Ruth Barshir et al.
The Transformer database [37] Yes Protein NA NA Yes http://bioinformatics.charite.de/transformer Michael F Hoffmann et al.
IntAct [38] No Protein and gene Multiple organisms NA Part http://www.ebi.ac.uk/intact Sandra Orchard
The extracellular matrix interaction database (MatrixDB) [39] No Protein Multiple organisms 106,543 Yes http://matrixdb.ibcp.fr G Launay et al.
A draft network of ligand-receptor-mediated [40] No Protein and gene Homo sapiens 2950 Part http://fantom.gsc.riken.jp/5/ Ramilowski et al.
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) [41] Yes Protein Multiple organisms NA Part http://rcsb.org Peter W Rose et al.
The DifferentialNet database [42] No Protein Homo sapiens NA No http://netbio.bgu.ac.il/diffnet/ Omer Basha et al.
Protein–Protein Interaction Sitesbase (PPInS) [43] Yes Protein NA 32,468 Part http://www.cup.edu.in:99/ppins/home.php Vicky Kumar et al.
UniLectin3D [44] Yes Protein NA NA Part https://www.unilectin.eu/unilectin3D François Bonnardel et al.
Ligand/Receptor Interaction Database (LRdb) [45] No Protein and gene Homo sapiens 3085 Yes https://github.com/SCA-IRCM/LRdb Simon Cabello-Aguilar et al.
CellPhoneDB [46] Yes Protein and gene Homo sapiens 1396 Part https://www.cellphonedb.org/ Mirjana Efremova et al.
CellTalk Database (CellTalkDB) [47] No Protein Homo sapiens, Mouse 5431 Yes http://tcm.zju.edu.cn/celltalkdb Xin Shao et al.
  1. Ligand-receptor complexes: if the structures of ligand-receptor comlpexes were considered by the databases
  2. Verified: if the pairs in these databases have been verified
  3. NA not available