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BioCRF is an implementation of
Grammatical-Restrained Hidden Conditional Random Fields (GRHCRFs), an extension of linear Hidden-Condtional Random Fields to include prior knowledge about the problem at hand by means of a regular grammar. This results very useful in several Bioinformatics problems where only solution that agree with a regular grammar rules are biologically meaningful.
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DisLocate
DisLocate is a method based on Grammatical-Restrained Hidden Conditional Random Fields (GRHCRFs) and Support Vector Regression (SVR) for the prediction of cysteine connectivity patterns in a protein chain. The method takes advantage of the protein subcellular localization as predicted by the BaCelLo predictor.
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BetAware is a web server for TransMembrane β-Barrel (TMBB) detection and tooplogy prediction. Both prediction steps are based on advanced machine-learning methods. For TMBB detection, BetAware exploits a new machine learning approach based on N-to-1 Extreme Learning Machines, while TMBB topology prediction is carried-out using a probabilistic model based on Grammatical-Restrained Hidden Conditional Random Fields, a discriminative framework introduced to address sequence labelling tasks in Bioinformatics.
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BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence. BCov is based on the PSICOV residue contact predictor, dynamic-programming algorithm for beta-strand alignments and integer programming for beta-sheet topology prediction.
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TPpred 2.0 is a web server for MITOCHONDRIAL targeting peptides prediction in proteins. TPpred 2.0 is optimized for the prediction of cleavage sites of mitochondrial targeting peptides.
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TPpred 3.0 is a web server for organelle targeting peptides prediction and discrimination in proteins. TPpred 3.0 is optimized for the prediction of cleavage sites of both mitochondrial and chloroplastic targeting peptides.
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Web server for the prediction of the impact of mutations on protein stability from sequence and structure.
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Web server for the prediction of protein sub-chloroplastic localization. SChloro is able to classify a query protein into six different chloroplastic sub-compartments: inner membrane, outer membrane, stroma, thylokoid lumen, thylakoid membrane and plastoglobule. SChloro also performs multi-label classification.
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Web server for the prediction of protein-protein interaction sites on unbound protein chainsn. Starting from protein 3D structure, ISPRED4 identifies those residues located on the chain surface that are likely to be PPI sites.
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Web server for the prediction of secretory signal peptides from protein sequences.
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Web server for the prediction of protein subcellular localization.