About PredictProtein

PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges. Listed below is a comprehensive list of methods and databases currently incorporated into the server.

Citing PredictProtein

If you find PreidctProtein useful please cite the paper along with the specific method you used (see Integrated Methods section below for citing info for specific methods).

  2014 (1)
PredictProtein---an open resource for online prediction of protein structural and functional features. Yachdav, G.; Kloppmann, E.; Kajan, L.; Hecht, M.; Goldberg, T.; Hamp, T.; Hönigschmid, P.; Schafferhans, A.; Roos, M.; Bernhofer, M.; and others Nucleic acids research, gku366. 2014.
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Integrated Methods

Method Name Description Reference Web Server Download
PROFphd Prediction of secondary structure and solvent accessibility - - ftp://rostlab.org/profphd
PHDhtm Prediction of transmembrane helices - - ftp://rostlab.org/profphd
PROFtmb Prediction of transmembrane beta-barrels - - ftp://rostlab.org/proftmb
NORSp Predictor of non-regular secondary structure - - ftp://rostlab.org/norsp
NCOILS Calculates the probability that the sequence will adopt a coiled-coil conformation - - -
SEG Identifies low complexity regions - - -
DISULFIND Prediction of disulfide bridges - - ftp://rostlab.org/profbval
PROFBval Prediction of residue mobility - - ftp://rostlab.org/profbval
NorsNet Prediction protein disordered sites - - ftp://rostlab.org/norsnet
UCON Contact based prediction of disordered sites - -
METADISORDER Consensus based prediction of protein disorder - -
InteractionSites Prediction of protein-protein interaction sites - -
LocTree2 Prediction of sub-cellular localization for all domains of life - - -
MetaStudent Prediction of GO terms for Molecular Function and Biological Process - - ftp://rostlab.org/metastudent
SNAP2 Prediction of functional changes due to single nucleotide polymorphism - - -
ConSurf Prediction of functional changes due to single nucleotide polymorphism - - -

Supporting Databases

Database Name Description Reference Download
UniRef Used for sequence homology searches by PSI-BLAST abstract http://www.uniprot.org/help/uniref
PDB The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. abstract http://www.rcsb.org/pdb/download/download.do
Pfam A collection of protein families abstract ftp://ftp.sanger.ac.uk/pub/databases/Pfam/releases/
PROSITE Database of biologically significant sites, patterns and profiles abstract ftp://ftp.expasy.org/databases/prosite/