Despite all the study of specificity of endopeptidases, it is still difficult if not impossible to predict where a native protein will be cleaved by a given enzyme. Amongst other factors, the tertiary structure of the substrate is important, and data obtained with small peptide substrates commonly do not relate directly to those for proteins. However, this search will allow the user to find cleavage sites for peptides, polypeptides and proteins in our collection of data from the literature. A description of the standard terminology for the specificity subsites of peptidases can be found here.
Please specify a peptide bond cleavage by selecting symbols to populate one or more of the boxes located on each side of the bond to be cleaved (marked 
). The symbols define the structure of the substrate, and their meanings are described fully below. The final specification will contain three elements. These have default settings that assume endopeptidase cleavage, so positions that contain unspecified amino acids may be left blank, but for an exopeptidase, one or two free termini must be indicated with TER. The three elements are:
A single symbol is needed, and the system will use XXX by default. Other symbols that are valid for this element include: BLK, PEP, TER. More specific symbols for individual N-terminal blocking groups exist if needed (ABZ, AC, AHX, BOC, BZ, CPP, DAA, DNP, DNS, FA, FOR, GAB, GLP, MCA, MCC, MSU, PZ, SUC, TOS, Z).
This will consist of one to eight of the symbols for amino acid residues. The default is XAA. Valid symbols are selected from those for normal amino acids (ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL), modified or abnormal amino acids (CHA, CYA, DAL, DAR, DFH, DHA, DHB, DLY, DPA, DPH, DPR, DSE, DVA, GLT, HYP, LYD, NAL, NLE, NPH, NVA, PIP, THE, TYS), those for sets of amino acids (ACI, ALI, ARO, ASX, BAS, GLX, HYD), or XAA for any single amino acid.
A single symbol is needed, and the system will use XXX by default. Other symbols that are valid for this element include: BLK, PEP, TER, and more specific symbols for individual C-terminal blocking groups exist if needed (AMC, BZN, EDD, MNA, NAE, NAN, NAO, NAP, NBA, NH2, OET, OME, ONA, OPH, P4P, PAB, PNA, SBZ).
We use the standard three-letter symbols for natural L-amino acids: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL. Additional symbols are:
| Symbol | Definition | May be N-terminal | May be C-terminal |
|---|---|---|---|
| ABZ | o-aminobenzoyl | Yes | No |
| AC | acetyl | Yes | No |
| Ac2 | N[alpha]N[epsilon]-diacetyl | Yes | No |
| ACI | acidic amino acid | No | No |
| AHX | 2-aminohexanoic acid | Yes | No |
| ALI | aliphatic amino acid | No | No |
| AMC | 7-(4-methyl)coumarylamide | No | Yes |
| ARO | aromatic amino acid | No | No |
| ASX | aspartate or asparagine | No | No |
| BAS | basic amino acid | No | No |
| BLK | any blocking group (N- or C-terminal) | Yes | Yes |
| BOC | t-butyloxycarbonyl | Yes | No |
| BZ | benzoyl | Yes | No |
| BZN | benzylamide | No | Yes |
| CHA | D-cyclohexylalanine | No | No |
| CPP | carboxyphenylpropionyl | Yes | No |
| CYA | cysteic acid | No | No |
| DAL | D-alanine | No | No |
| DAP | meso-2,6-diaminopimelyl | No | No |
| DAR | D-arginine | No | No |
| DFH | dehydrophenylalanine | No | No |
| DGl | D-Glu | No | No |
| DHA | dehydroalanine | No | No |
| DHB | dehydrobutyrine | No | No |
| DLa | D-lactate | No | No |
| DLY | D-lysine | No | No |
| DLZ | (epsilon-benzyloxycarbonyl)-D-lysine | No | No |
| DNP | 2,4-dinitrophenyl | Yes | No |
| DNS | 5-dimethylaminonaphthyl-1-sulfonyl; "dansyl" | Yes | No |
| DPA | (2,4-dinitrophenyl)-L-2,3-diaminopropionyl | No | No |
| DPH | D-phenylalanine | No | No |
| DPR | D-proline | No | No |
| DSE | D-serine | No | No |
| DVA | D-valine | No | No |
| EDD | N-(2,4-dinitrophenyl)ethylenediamine | No | Yes |
| FA | furylacryloyl | Yes | No |
| FMK | 7-amino-4-trifluoromethylcoumarin | No | Yes |
| FOR | formyl | Yes | No |
| GAB | gamma-amino-n-butyric acid | No | No |
| GLP | pyrrolidone carboxylyl; pyroglutamyl | Yes | No |
| GLT | glutaryl | Yes | No |
| GLX | glutamate or glutamine | No | No |
| HYD | hydrophobic amino acid | No | No |
| HYP | hydroxyproline | No | No |
| LYD | lysine(2,4-dinitrophenyl) | No | No |
| MCA | (7-methoxy-coumarin-4-yl)acetyl | Yes | No |
| MCC | 7-methoxycoumarin-3-carboxylyl | Yes | No |
| MCH | methoxycarbonyl-cyclo-hexylglycyl | Yes | No |
| MES | methane-sulfonyl | Yes | No |
| MNA | 2-(4-methoxy)naphthylamide | No | Yes |
| MSU | methoxysuccinyl | Yes | No |
| NAE | 2,4-dinitroanilinoethylamide | No | Yes |
| NAL | beta-naphthylalanine | No | No |
| NAN | 4-nitroanilide | No | Yes |
| NAP | 2-naphthylamide | No | Yes |
| NBA | nitrobenzylamide | No | Yes |
| NH2 | amide | No | Yes |
| NLE | norleucine | No | No |
| NPH | 4-nitrophenylalanine | No | No |
| NVA | norvaline | No | No |
| OET | ethyl ester | No | Yes |
| OME | methyl ester | No | Yes |
| ONA | 4-nitrophenyl ester | No | Yes |
| OPH | phenyl ester | No | Yes |
| P4P | 4-pyridinium alkoxy | No | Yes |
| PAB | p-aminobenzoate | No | Yes |
| PEP | peptide (any length) | Yes | Yes |
| PIP | pipecolyl | No | No |
| PIN | piperidine amide | No | No |
| PZ | (4-phenylazo)benzyloxycarbonyl | Yes | No |
| SBZ | thiobenzyl ester | No | Yes |
| SUC | 3-carboxypropionyl (succinyl) | Yes | No |
| TER | free N- or C-terminus | Yes | Yes |
| TOS | toluene-p-sulfonyl; "tosyl" | Yes | No |
| TYS | Tyr(SO3H) | No | No |
| XAA | any single amino acid | No | No |
| XXX | any group(s) (any number) | Yes | Yes |
| Z | benzyloxycarbonyl | Yes | No |