Links   

This table provides detailed links and descriptions with respect to previously developed servers or softwares for protease substrate cleavage sites prediction.

Note that among them, three are general cleavage site prediction servers (PeptideCutter, PoPS and SitePrediction), the others are family-specific servers that were specifically designed to model and predict the substrate specificity for a particular protease, such as PEPS, CasPredictor, GraBCas, CASVM and Cascleave.

 

Predictors	Description	URL address	Features
PeptideCutter	Predict potential cleavage sites cleaved by proteases or chemicals	http://au.expasy.org/tools/peptidecutter/	Amino acid occurrence
PEPS	Rule-based endopeptidase cleavage site scoring matrices and predict paspase-3 substrates	not available	Position-specific scoring matrices (PSSM)
CasPredictor	Predict Caspase cleavage sites	http://icb.usp.br/~farmaco/Jose/CaSpredictorfiles	Amino acid substitution, amino acid frequency and the presence of ' PEST' sequences was used as the input features
GraBCas	Position-specific scoring prediction of cleavage sites for caspase 1-9 and granzyme B	http://wwwalt.med-rz.uniklinik-saarland.de/med_fak/humangenetik/software/index.html	Improved position specific scoring scheme
CASVM	SVM-based prediction of caspase cleavage sites	http://casbase.org/casvm/index.html	SVM classifiers trained with sequence segments containing the tetrapeptide cleavage sites
PoPS	Prediction of protease specificity	http://pops.csse.monash.edu.au/pops-cgi/	Amino acid occurrence, Position-specific scoring matrices (PSSM), predicted structure information such as substrate secondary structure and solvent accessibility
Cascleave	Predict substrate cleavage site of caspases	http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/Cascleave/	Multiple sequential and structural features including local amino acid sequence profile, predicted solvent accessibility and native disorder features
SitePrediction	Predicting the cleavage of proteinase substrastes	http://www.dmbr.ugent.be/prx/bioit2-public/SitePrediction/	Amino acid occurrence, 'PEST' sequences, and structural information such as secondary structure and solvent accessibility