Brief introduction to PredictProtein

Database searches:

1. generation of multiple sequence alignments ( MaxHom)
2. detection of functional motifs ( PROSITE)
3. detection of composition-bias ( SEG)
4. detection of protein domains ( PRODOM)
5. fold recognition by prediction-based threading ( TOPITS)

Predictions of:

1. secondary structure ( PHDsec, and PROFsec)
2. residue solvent accessibility ( PHDacc, and PROFacc)
3. transmembrane helix location and topology ( PHDhtm, PHDtopology)
4. protein globularity ( GLOBE)
5. coiled-coil regions ( COILS)
6. cysteine bonds ( CYSPRED)
7. structural switching regions ( ASP)

Evaluation of secondary structure prediction accuracy ( EvalSec)

• See also: EVA : an automatic evaluation of prediction methods

Brief introduction to META PredictProtein

Database searches:

1. prediction-based threading, also incorporating purely sequence-based database searches (FRSVR)
2. hidden Markov model method (SAM-T98) for finding remote homologs of protein sequences (SAMT98)

Predictions of:

1. presence and location of signal peptide cleavage sites in amino acid sequences from different organisms (SignalP )
2. mucin type GalNAc O-glycosylation sites in mammalian proteins (NetOglyc )
3. cleavage sites of picornaviral proteases (NetPicoRNA )
4. whether or not a protein contains an N-terminal chloroplast transit peptide, cTP, and of probable sites for cleavage of the transit peptide (ChloroP)
5. secondary structure consensus between various methods (JPRED)
6. location and orientation of transmembrane helices (TMHMM)
7. location and orientation of transmembrane helices (TOPPRED)
8. location of transmembrane helices (DAS)
9. 3D structure by homology modelling (automated modelling, SWISS-MODEL)
10. 3D structure by homology modelling using a collection of methods and databases developed to predict protein structures (CPHmodels)