PSIPRED Publications

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

The PSIPRED server

  • Buchan DWA, Jones DT (2019). The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Research.

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.


  • 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.


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


  • 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.


  • Kandathil SM, Greener JG, Jones DT (2019). Prediction of inter-residue contacts with DeepMetaPSICOV in CASP13. Proteins.


  • Greener JG, Kandathil SM, Jones DT (2019). Extending genome-scale de novo protein modelling coverage using iterative deep learning-based prediction of structural constraints. Bioarxiv.


  • 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.


  • 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.


  • 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.


  • 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.


  • 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.


  • 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.