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.
|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|