About PredictProtein
PredictProtein is an Internet service for sequence analysis and the prediction of protein structure and function. Users submit protein sequences or alignments; PredictProtein returns multiple sequence alignments, PROSITE sequence motifs, low-complexity regions (SEG), nuclear localisation signals, regions lacking regular structure (NORS) and predictions of secondary structure, solvent accessibility, globular regions, transmembrane helices, coiled-coil regions, structural switch regions, disulfide-bonds, sub-cellular localization, and functional annotations.Upon request fold recognition by prediction-based threading, CHOP domain assignments, predictions of transmembrane strands and inter-residue contacts are also available. For all services, users can submit their query either by electronic mail, or interactively from World Wide Web.
Publications
PredictProtein: B Rost,G Yachdav and J Liu (2004) The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.
- Author: B Rost
- Contact: yachdav@maple.bioc.columbia.edu
- URL: http://www.rostlab.org
- Version: 10.20.04
- Description: PredictProtein is the acronym for all prediction programs run.
PROSITE: A Bairoch, P Bucher & K Hofmann (1997) Nucleic Acids Research, 25:217-221
- Author: A Bairoch, bairoch@cmu.unige.ch P Bucher & K Hofmann
- Contact: bairoch@cmu.unige.ch
- URL: http://www.expasy.ch/prosite
- Version: 99.07
- Description: PROSITE is a database of functional motifs.
ScanProsite, finds all functional motifs in your sequence that are
annotated in the ProSite db.
SEG: J C Wootton & S Federhen (1996) Methods in Enzymology, 266:554-571
- Author: J C Wootton & S Federhen, wootton@ncbi.nlm.nih.gov
- Contact: rost@columbia.edu
- URL: wootton@ncbi.nlm.nih.gov
- Version: 1994
- Description: SEG divides sequences into regions of low-, and
high-complexity. Low-complexity regions typically correspond to 'simple
sequences' or 'compositionally-biased' regions.
ProDom: ELL Sonnhammer & D Kahn (1994) Protein Science, 3:482-492
- Author: LL Sonnhammer; J Gouzy, F Corpet, F Servant, D Kahn, dkahn@zyx.toulouse.inra.fr
- Contact: dkahn@zyx.toulouse.inra.fr
- URL: http://protein.toulouse.inra.fr/prodom.html
- Version: 2000.1
- Description: ProDom is a database of putative protein
domains. The database is searched with BLAST for domains corresponding
to your protein.
MaxHom: MaxHom: C Sander R Schneider (1991) Proteins, 9:56-68
- Author: C Sander & R Schneider, schneider@lion-ag.de
- Contact: schneider@lion-ag.de
- Version: 1.99.04
- Description: MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
MView: MView: N P Brown, C Leroy & C Sander (1998) Bioinformatics, 14:380-381
- Author: N Brown, nbrown@nimr.mrc.ac.uk
- URL: http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/
- Copyright: Copyright (C) Nigel P. Brown, 1997-1998. All rights reserved.
- Version: 1.40.2
- Description: MView is a program converting multiple sequence alignments into fancy HTML formatted output.
PHD: B Rost (1996) Methods in Enzymology, 266:525-539
- Author: B Rost
- Contact: rost@columbia.edu
- URL: http://www.rostlab.org
- Version: 1.96
- Description: PHD is a suite of programs predicting 1D
structure (secondary structure, solvent accessibility) from multiple
sequence alignments.
PHDsec: B Rost & C Sander (1993) J. of Molecular Biology, 232:584-599
- Author: B Rost
- Contact: rost@columbia.edu
- URL: http://www.rostlab.org
- Version: 1.96
- Description: PHDsec predicts secondary structure from multiple sequence alignments.
PHDacc: B Rost & C Sander (1994) Proteins, 20:216-226
- Author: B Rost
- Contact: rost@columbia.edu
- URL: http://www.rostlab.org
- Version: 1.96
- Description: PHDacc predicts per residue solvent accessibility from multiple sequence alignments.
PHDhtm: B Rost, P Fariselli & R Casadio (1996) Protein Science, 7:1704-1718
- Author: B Rost
- Contact: rost@columbia.edu
- URL: http://www.rostlab.org
- Version: 1.96
- Description: PHDhtm predicts the location and topology of transmembrane helices from multiple sequence alignments.
PROF: B Rost (2004) Meth. Mol. Biol., submitted.
- Author: B Rost
- Contact: rost@columbia.edu
- URL: http://www.rostlab.org
- Version: 2000_04
- Description: PROF is a suite of programs predicting 1D
structure (secondary structure, solvent accessibility) from multiple
sequence alignments.
PROFsec: B Rost (2004) Meth. Mol. Biol., submitted.
- Author: B Rost
- Contact: rost@columbia.edu
- URL: http://www.rostlab.org
- Version: 2000_04
- Description: PROFsec predicts secondary structure from multiple sequence alignments.
PROFACC: B Rost (2004) Meth. Mol. Biol., submitted.
- Author: B Rost
- Contact: rost@columbia.edu
- URL: http://www.rostlab.org
- Version: 2000_04
- Description: PROFacc predicts per residue solvent accessibility from multiple sequence alignments.
GLOBE: B Rost (1998) unpublished
DISULFIND: A.Ceroni, P.Frasconi, A.Passerini and A.Vullo (2004) Bioinformatics, 20, 653-659, 2004
- Author: A.Ceroni, P.Frasconi, A.Passerini and A.Vullo
- Contact: cystein@dsi.unifi.it
- URL: http://disulfind.dsi.unifi.it/
- Version: 1.2
- Description: DISULFIND is a disulphide bridges predictor based on a two steps process.
A conformational switch prediction program: Young et al. Protein Science(1999) 8:1752-64.
- Author: Young M, Kirshenbaum K, Dill KA and Highsmith S.
- Contact: mmyoung@sandia.gov, kent@cheme.caltech.edu, shighsmith@sf.uop.edu
- Version: 1.0
- Description: ASP finds regions that are most likely to behave as switches in proteins known to exhibit this behavior
HMMPFAM: Bateman et al. Nucleic Acids Research 2004 32:D138-D141.
- Author: Bateman A, Coin L, Durbin R, Finn RD, Hollich V,
Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL,
Studholme DJ, Yeats C, Eddy SR.
- Contact: agb@sanger.ac.uk
- Version: 2.2g
- Description: Search one or more sequences against HMM database
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