1 - 25 of 25 results

GPS-CCD / Calpain Cleavage Detector

Predicts calpain cleavage sites. GPS-CCD is a computational program that was used to annotate potential calpain cleavage sites for hundreds of calpain substrates, for which the exact cleavage sites had not been previously determined. The software is useful for pinpointing potential calpain cleavage sites, while computational predictions followed by experimental verification should lead to an improved identification of calpain substrates in the near future.

hfAIM / high fidelity AIM system

A web tool for in silico genome-wide prediction of Atg8 interacting motifs (AIMs) in proteins. Using hfAIM it is possible to perform fast and reliable genome-wide screening of AIM containing proteins that may be regulated by autophagy, and to select candidates for further studies using experimental approaches. This bioinformatics approach can facilitate a better understanding of the contribution of autophagy to multiple biological processes in various organisms.


A web application for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events. CleavPredict offers in silico prediction of cleavage sites specific for 11 human MMPs. The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results. To augment the substrate cleavage prediction process, CleavPredict provides information about the structural features of potential cleavage sites that influence proteolysis. These include: secondary structure, disordered regions, transmembrane domains, and solvent accessibility. The server also provides information about subcellular location, co-localization, and co-expression of proteinase and potential substrates, along with experimentally determined positions of single nucleotide polymorphism (SNP), and posttranslational modification (PTM) sites in substrates. All this information will provide the user with perspectives in reasoning about proteolytic events.


forum (1)
Provides easy integrated access to bioinformatics tools aiming to help researchers for assessing whether a protein is a potential functional LIR containing protein based solely on its amino acid sequence. Given an amino acid sequence as input, iLIR searches for instances of short sequences compliant with a refined sensitive regular expression pattern of the extended LIR motif (xLIR-motif) and retrieves characterized protein domains from the SMART database for the query. Additionally, iLIR scores xLIRs against a custom position-specific scoring matrix (PSSM) and identifies potentially disordered subsequences with protein interaction potential overlapping with detected xLIR-motifs.

PROSPER / PROtease Specificity Prediction servER

An integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database) with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes.


A web tool for predicting the cleavage sites of proproteins such as prohormones and neuropeptides. CleavePred's algorithm is powered by ASAP, a Machine-Learning framework for predicting local protein properties. This tool provides state-of-the-art results, with a low false-positive rate. CleavePred is suited for analyzing new proteomes at a genomic scale, and it is appropriate for a variety of organisms (including mammals and insects). Applying CleavePred will provide the user with a list of peptide candidates that may carry a bioactive function. It can be served as a complementary tool for Mass Spectrometry peptide analysis.


Retrieves information from REBASE restriction enzyme database. redata searches the REBASE database for information on a specified restriction enzyme. It writes an output file with information on the cut site and (optionally) the full list of isoschizomers (enzymes with the same target sequence), commercial suppliers of the enzyme and literature references. redata uses the EMBOSS REBASE restriction enzyme data files stored in directory data/REBASE/* under the EMBOSS installation directory.

Cascleave / Caspase substrate cleavage site prediction

Allows high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates. Cascleave aims to identify novel substrates and cleavage sites of caspases and granzyme B (GrB). It assists users to understand the functional roles of these important proteases in human proteolytic cascades. This tool employs a two-step integrative framework to characterize protein sequence.