Discriminative HMMs (Hidden Markov models) predicts localizations using motifs that are present in a compartment but absent in other, nearby, compartments by utilizing an hierarchical structure that mimics the protein sorting mechanism.
FastHMM and FastBLAST are fast heuristics to replace HMM search, InterProScan, and all-versus-all BLAST. FastHMM uses PSI-BLAST to quickly select likely members of the family and then uses HMMer to confirm those hits. FastBLAST relies on alignments of proteins to known families from FastHMM and from rpsblast against COG. FastBLAST uses these alignments to avoid most of the work of all-versus-all BLAST. FastBLAST further reduces the work by clustering similar sequences.
SLPFA is a predictor for subcellular location prediction of proteins by feature vectors based on amino acid composition (frequency) and sequence alignment. 90.96% of overall accuracy was obtained through fivefold cross validation tests with TargetP plant data sets.
SLPFA is an improved subcellular location predictor of SLP-Local
The INTREPED (INTeractive dna REPair prEDiction) web server is a collection of services for predicting properties relating to DNA repair. DNA repair is thought to exist in all organisms that have an active metabolism, and repair systems are crucial for repairing many types of DNA damage. External damage includes (but is not limited to) ionizing (UV) radiation, tobacco smoke, and chemical alteration. Examples of internal damage are DNA copying errors, oxygen byproducts resulting from metabolism, and hydrolysis.
PRORATE is a novel approach to predict protein folding rates for two-state and multi-state protein folding kinetics, which combines a variety of structural topology and complex network properties that are calculated from protein three-dimensional structures.
HSEpred is a web server to predict the HSE(Half-Sphere Exposure) measures and infer residue contact numbers using the predicted HSE values, based on a well-prepared non-homologous protein structure dataset.