Table 3.
List of minimotifs based databases.
| Web-applications | C-term only | Species | Type of dataset | # of functions | Reference |
|---|---|---|---|---|---|
| C-terminome | Yes | Homo sapiens | C-terminal minimotifs and Proteins | 3546 verified and ⁓9 million predicted | Sharma et al. (2016) |
| TopFIND3.0 | No | 5 species | Neo C-termini as from mass-spectrometry | 128 modifications, 130,182 proteolytic ends | Fortelny et al. (2015) |
| ProTeus | Yes | None specified | Signature groups in Swiss-Prot | Unknown (all predicted) | Gnad et al. (2012) |
| ELM | No | All | Short linear motifs anywhere in proteins | >275 motif classes and >300 motif instances | Dinkel et al. (2012) |
| MnM | No | All | Minimotifs anywhere in proteins | 1,060,436 instances | Lyon et al. (2018) |
| DILIMOT | No | None specified | Discovery-based tool to identify motifs in a protein sequence based on homology | None specified | Neduva and Russell (2006) |
| Proteolysis | |||||
| MEROPS | No | Many | Peptidase, peptidase substrates | 92,216 cleaved products; 908,326 peptidases | Rawlings et al. (2014) |
| CutDB | No | All | Proteolytic events, both actual and predicted | 3070 proteolytic events; 470 proteases | Igarashi et al. (2007) |
| TOPPR | No | human and mouse | Published proteolytically processed sites in human and mouse proteins based on MS/MS | Proteolysis sites | Colaert et al. (2013) |
| Binding | |||||
| PDZBase | Yes | None specified | PDZ-domain interaction with protein s | 300 interactions | Beuming et al. (2005) |
| Binding DB | No | None specified | Protein: drug molecules interactions | 1,391,403 binding data, for 7225 protein targets and 621,060 small molecules | Liu et al. (2007) |
| Post-translational modification0073 | |||||
| SwissProt | No | All | PTM, protein sequences | 556,196 entries on protein sequences | Boeckmann et al. (2003) |
| O-Glycbase | No | All | O-linked glycosylation sites | 242 glycoprotein entries | Gupta et al. (1999) |
| PHOSIDA | No | 9 species | Phosphorylation, acetylation and N-glycosylation site database | more than 60,000 sites | Gnad et al. (2011) |
| Phospho3D | No | All | 3D structures for phosphorylation site database | 5314 phosphorylation sites in 1805 sequences | Zanzoni et al. (2007) |
| PhosphoSite-Plus | No | Mammal | PTMs | 330,000 non-redundant | Hornbeck et al. (2015) |
| dbPTM | No | None specified | Integrated resource from 14 public databases on PTMs | 610,037 experimental and 546,911 putative PTM sites | Lu et al. (2013) |
| Human Histone Modification Database | No | Human | Histone modification database. | 43 modification types | Zhang et al. (2010) |