PSIPRED Publications

Please use the following references when citing the PSIPRED server and its methods

The PSIPRED server

  • Buchan DWA, Minneci F, Nugent TCO, Bryson K, Jones DT. (2013). Scalable web services for the PSIPRED Protein Analysis Workbench . Nucleic Acids Research .  41 (W1): W340-W348.

The PSIPRED secondary structure prediction method

  • Jones DT. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.

DISOPRED

  • Jones DT, Cozzetto D. (2015). DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinformatics. 2015 Mar 15;31(6):857-63. doi: 10.1093/bioinformatics/btu744. Epub 2014 Nov 12.

MEMSAT

  • Nugent, T. & Jones, D.T. (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics. 10, 159. Epub

GenTHREADER, pGenTHREADER, pDomTHREADER

  • Lobley, A., Sadowski, M.I. & Jones, D.T. (2009) pGenTHREADER and pDomTHREADER: New Methods For Improved Protein Fold Recognition and Superfamily Discrimination. Bioinformatics. 25, 1761-1767.
  • McGuffin LJ & Jones DT. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881.

MetaPSICOV2

  • Buchan DWA, Jones DT (2018). Improved protein contact predictions with the MetaPSICOV2 server in CASP12. Proteins. 2018 Mar;86 Suppl 1:78-83. doi: 10.1002/prot.25379. Epub 2017 Sep 29.

MEMPACK

  • Nugent T, Ward S, Jones DT (2011). The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinformatics. 2011 May 15;27(10):1438-9. doi: 10.1093/bioinformatics/btr096. Epub 2011 Feb 23.

Dompred

  • Bryson K, Cozzetto D, Jones DT (2007). Computer-assisted protein domain boundary prediction using the DomPred server. Curr Protein Pept Sci. 2007 Apr;8(2):181-8.

Bioserf and Domserf

  • Buchan DW, Minneci F, Nugent TC, Bryson K, Jones DT (2013). Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W349-57. doi: 10.1093/nar/gkt381. Epub 2013 Jun 8.

FFPred

  • Cozzetto D, Minneci F, Currant H, Jones DT (2016). FFPred 3: feature-based function prediction for all Gene Ontology domains. Sci Rep. 2016 Aug 26;6:31865. doi: 10.1038/srep31865.

HSPred

  • Lise S, Buchan D, Pontil M, Jones DT (2011). Predictions of hot spot residues at protein-protein interfaces using support vector machines. PLoS One. 2011 Feb 28;6(2):e16774. doi: 10.1371/journal.pone.0016774.

MEMEMBED

  • Nugent T, Jones DT (2013). Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics. 2013 Sep 18;14:276. doi: 10.1186/1471-2105-14-276.

METSITE

  • Sodhi JS, Bryson K, McGuffin LJ, Ward JJ, Wernisch L, Jones DT (2004). Predicting metal-binding site residues in low-resolution structural models. J Mol Biol. 2004 Sep 3;342(1):307-20.