References
- 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: help@predictprotein.org
- URL: http://www.predictprotein.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: help@predictprotein.org
- 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.
- PHD: B Rost (1996) Methods in Enzymology, 266:525-539
- Author: B Rost
- Contact: help@predictprotein.org
- URL: http://cubic.bioc.columbia.edu
- 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: help@predictprotein.org
- URL: http://cubic.bioc.columbia.edu
- 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: help@predictprotein.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: help@predictprotein.org
- URL: http://cubic.bioc.columbia.edu
- 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: help@predictprotein.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: help@predictprotein.org
- URL: http://cubic.bioc.columbia.edu
- Version: 2000_04
- Description: PROFsec predicts secondary structure from multiple sequence alignments.
- PROFACC: B Rost (2004) Meth. Mol. Biol., submitted.
- Author: B Rost
- Contact: help@predictprotein.org
- URL: http://cubic.bioc.columbia.edu
- 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
- 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
- DISULFIND: A.Ceroni, P.Frasconi, A.Passerini and A.Vullo (2004) Bioinformatics, 20, 653-659, 2004
- NORS: Liu J, Rost B (2003) NORSp: predictions of long regions without regular secondary structure. Nucleic Acids Research 31(13):3833-3835
- CHOP: Liu J ∧ Rost B (2004) CHOP proteins into structural domain-like fragments. Proteins, 55(3):678-688
- ISIS: Yanay Ofran and Burkhard Rost (2007). ISIS: Interaction Sites Identified from Sequence. Bioinformatics. 23 (2), e13-e16
- DISIS: Yanay Ofran and Venkatesh Mysore and Burkhard Rost (2007). Prediction of DNA-binding residues from sequence. Bioinformatics. 23 (13), i347-i353
- NORSnet: Avner Schlessinger and Jinfeng Liu and Burkhard Rost (2007). Natively unstructured loops differ from other loops. PLoS Computational Biology. 3 (7), e140.
- Author: A. Schlessinger
- Contact: Avner Schlessinger
- URL: http://predictprotein.org/
- Version: 1.0.4
- Description: Identifies unstructured loops from sequence.
- PROFbval: Avner Schlessinger and Guy Yachdav and Burkhard Rost (2006). PROFbval: predict flexible and rigid residues in proteins. Bioinformatics. 22 891-893.
- METADISORDER: A. Schlessinger and M. Punta and G. Yachdav and L. Kajan and B. Rost (2009). Improved disorder prediction by combination of orthogonal approaches. PLoS One. 4 (2), e4433.
- PROFcon: Marco Punta and Burkhard Rost (2005). PROFcon: novel prediction of long-range contacts. Bioinformatics. 21 (13), 2960-2968
- PROFtmb: Henry Bigelow and Burkhard Rost (2006). PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Research. 34 (Web Server issue), W186-188.
- SNAP: Yana Bromberg and Guy Yachdav and Burkhard Rost (2008). SNAP predicts effect of mutations on protein function. Bioinformatics. in press.
- LOCtree: Rajesh Nair and Burkhard Rost (2005). Mimicking cellular sorting improves prediction of subcellular localization. Journal of Molecular Biology. 348 (1), 85-100