※Computational resources of protein cleavage, etc.:
Last updated: Feb. 26th, 2011
<1> Other resource of calpains and calpain-mediated cleavage.
<2> Other resource of protein cleavage
A. Proteases and Protease-mediated cleavage
3. The Degradome database: the peptidase database, which contains information on peptidases and inhibitors among organisms, substrate cleavage sites and indexes for expressed sequence tag libraries containing peptidases .(Quesada, et al., 2009).
4. Serine Proteases: a database of serine proteases.
6. PeptideMass: cleaves a protein sequence from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides.(Wilkins, et al., 1997).
B. Signal peptide cleavage sites
2. PCLR: a method of predicting chloroplast localization of proteins in plant cells. The prediction algorithm was trained using principal component logistic regression with stepwise variable selection (Schein, et al., 2001).
3. LipoP: a web server produces predictions of lipoproteins and discriminates between lipoprotein signal peptides, other signal peptides and n-terminal membrane helices in Gram negative bacteria (Juncker, et al., 2003).
7. PATS: PATS identifies amino acid sequences that are potentially targeted to the apicoplast matrix of Plasmodium falciparum. Note that secondary analysis of candidate sequences is required for confirmation (Waller, et al., 1998; Zuegge, et al., 2001).
14. SignalP: a web server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models (Nielsen, et al., 1999; Bendtsen, et al., 2004; Emanuelsson, et al., 2007; Nielsen, et al., 1997; Menne, et al., 2000).
15. TatP 1.0: a web server predicts the presence and location of Twin-arginine signal peptide cleavage sites in bacteria. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of two artificial neural networks. A postfiltering of the output based on regular expressions is possible (Bendtsen, et al., 2005).
16. ProP 1.0: a web server predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase (PC) prediction (Duckert, et al., 2004).
17. TargetP 1.1: a web server predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP) (Nielsen, et al., 1997; Emanuelsson, et al., 2000).
19. NetCorona 1.0: a web server predicts coronavirus 3C-like proteinase (or protease) cleavage sites using artificial neural networks on amino acid sequences. Every potential site is scored and a list is compiled in addition to a graphical representation. Refer to publication for more detailed information and performance values (Kiemer, et al., 2004).
20. NetPicoRNA 1.0: a web server produces neural network predictions of cleavage sites of picornaviral proteases. The method is described in detail in the reference article mentioned below (see CITATIONS at the bottom of this page) (Blom, et al., 1996).
21. SecretomeP 2.0: a web server produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion. The method queries a large number of other feature prediction servers to obtain information on various post-translational and localizational aspects of the protein, which are integrated into the final secretion prediction (Bendtsen, et al., 2004; Bendtsen, et al., 2005).
23. PeptideCutter: a web server predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. PeptideCutter returns the query sequence with the possible cleavage sites mapped on it and /or a table of cleavage site positions (Wilkins, et al., 1999).
C. Caspase substrates cleavage
3. PEPS: is a tool for the prediction of caspase caspase cleavage sites. It is based on the consensus motifs for caspase substrates. Software can be obtained upon request from author (Lohmuller, et al., 2003).
is a software tool for the prediction of caspase
cleavage sites which utilizes position-specific
scoring matrices together with indices based
on neighboring PEST sequences. Software can
be obtained upon request from author (Garay-Malpartida, et al., 2005).
D. Proteasomal cleavage