References

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. GLOBE: B Rost (1998) unpublished
    • Author: B Rost
    • Contact: help@predictprotein.org
    • URL: http://cubic.bioc.columbia.edu/papers/1999_globe/paper.html
    • Version: 1.98.05
    • Description: GLOBE predicts the globularity of a protein
13. 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://cassandra.dsi.unifi.it/cysteines/index.html
    • Version: 2.0
    • Description: DISULFIND is a disulphide bridges predictor based on a two steps process.
14. 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
15. 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
16. 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://cassandra.dsi.unifi.it/cysteines/index.html
    • Version: 2.0
    • Description: DISULFIND is a disulphide bridges predictor based on a two steps process.
17. NORS: Liu J, Rost B (2003) NORSp: predictions of long regions without regular secondary structure. Nucleic Acids Research 31(13):3833-3835
    • Author: J. Liu
    • Contact: Jinfeng Liu
    • URL: http://cubic.bioc.columbia.edu/services/NORSp/
    • Version: 1.0
    • Description: NORSp is a predictor of NOn-Regular Secondary Structure.
18. CHOP: Liu J ∧ Rost B (2004) CHOP proteins into structural domain-like fragments. Proteins, 55(3):678-688
    • Author: J. Liu
    • Contact: Jinfeng Liu
    • URL: http://cubic.bioc.columbia.edu/services/chop/
    • Version: 1.0
    • Description: CHOP is a method of dissecting proteins into domain-like fragments based on sequence homology.
19. ISIS: Yanay Ofran and Burkhard Rost (2007). ISIS: Interaction Sites Identified from Sequence. Bioinformatics. 23 (2), e13-e16
    • Author: Y. Ofran
    • Contact: Yanay Ofran
    • URL: http://cubic.bioc.columbia.edu/services/isis/
    • Version: 1.0
    • Description: Prediction of residues involved in external protein-protein interactions.
20. DISIS: Yanay Ofran and Venkatesh Mysore and Burkhard Rost (2007). Prediction of DNA-binding residues from sequence. Bioinformatics. 23 (13), i347-i353
    • Author: Y. Ofran
    • Contact: Yanay Ofran
    • URL: http://cubic.bioc.columbia.edu/services/disis/
    • Version: 1.0
    • Description: Prediction of residues involved in DNA binding.
21. 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.
22. PROFbval: Avner Schlessinger and Guy Yachdav and Burkhard Rost (2006). PROFbval: predict flexible and rigid residues in proteins. Bioinformatics. 22 891-893.
    • Author: A. Schlessinger
    • Contact: Avner Schlessinger
    • URL: http://cubic.bioc.columbia.edu/newwebsite/services/Profbval
    • Version: 1.0.4
    • Description: Prediction of protein flexibility and rigidity prediction from sequence.
23. 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.
    • Author: A. Schlessinger
    • Contact: Avner Schlessinger
    • URL: http://cubic.bioc.columbia.edu/newwebsite/services/md/index.php
    • Version: 1.0.3
    • Description: Protein disorder prediction based on orthogonal sources of information.
24. PROFcon: Marco Punta and Burkhard Rost (2005). PROFcon: novel prediction of long-range contacts. Bioinformatics. 21 (13), 2960-2968
    • Author: M. Punta
    • Contact: Marco Punta
    • URL: http://cubic.bioc.columbia.edu/services/profcon/
    • Version: 1.0
    • Description: contact prediction method.
25. 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.
    • Author: H. Bigelow
    • Contact: Henry Bigelow
    • URL: http://cubic.bioc.columbia.edu/services/proftmb/
    • Version: 1.1.1
    • Description: per-residue prediction of bacterial transmembrane beta barrels.
26. SNAP: Yana Bromberg and Guy Yachdav and Burkhard Rost (2008). SNAP predicts effect of mutations on protein function. Bioinformatics. in press.
    • Author: Y. Bromberg
    • Contact: Yana Bromberg
    • URL: http://cubic.bioc.columbia.edu/services/snap/
    • Version: 1.0.8
    • Description: a method for evaluating effects of single amino acid substitutions on protein function.
27. LOCtree: Rajesh Nair and Burkhard Rost (2005). Mimicking cellular sorting improves prediction of subcellular localization. Journal of Molecular Biology. 348 (1), 85-100
    • Author: R. Nair
    • Contact: Rajesh Nair
    • URL: http://cubic.bioc.columbia.edu/services/loctree/
    • Version: 1.0.3
    • Description: predict the subcellular localization of proteins.