Server for the prediction of structural aspects of protein residues

PSP server contains a collection of web services that address several protein structure prediction (PSP) sub-problems. Each of these sub-problems focuses on a single structural feature of a protein and the PSP server is using a Learning Classifier System to predict them for a given sequence of amino acids.

The structural features predicted by the PSP server are:

• density of packing of different parts of a protein,
• how buried/exposed, far/close to the surface are different residues within a protein,
• classic measures such as coordination number or solvent accessibility,
• metrics derived from modelling the protein structure using topological and geometrical properties.

Publications

• DOI eprint slides BibTeX
  J. Bacardit, P. Widera, A. Marquez-Chamorro, F. Divina, J.S. Aguilar-Ruiz, N. Krasnogor
  Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features
  in Bioinformatics, 28(19):2441-2448, October 2012

  @ARTICLE{Bacardit2012,
    title = {Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features},
    author = {Bacardit, J. and Widera, P. and Marquez-Chamorro, A. and Divina, F. and Aguilar-Ruiz, J. S. and Krasnogor, N.},
    year = 2012,
    doi = {10.1093/bioinformatics/bts472},
    month = oct,
    journal = {Bioinformatics},
    volume = {28},
    number = {19},
    pages = {2441--2448}
  }
  

• DOI BibTeX
  M. Stout, J. Bacardit, J.D. Hirst, R.E. Smith, N. Krasnogor
  Prediction of topological contacts in proteins using learning classifier systems
  in Soft Computing, 13(3):245-258, February 2009

  @ARTICLE{Stout2009,
    title = {Prediction of topological contacts in proteins using learning classifier systems},
    author = {Stout, Michael and Bacardit, Jaume and Hirst, Jonathan D. and Smith, Robert E. and Krasnogor, Natalio},
    year = 2009,
    doi = {10.1007/s00500-008-0318-8},
    month = feb,
    journal = {Soft Computing},
    volume = {13},
    number = {3},
    pages = {245--258}
  }
  

• DOI BibTeX
  M. Stout, J. Bacardit, J.D. Hirst, N. Krasnogor
  Prediction of recursive convex hull class assignments for protein residues
  in Bioinformatics, 24(7):916-923, April 2008

  @ARTICLE{Stout2008,
    title = {Prediction of recursive convex hull class assignments for protein residues},
    author = {Stout, M. and Bacardit, J. and Hirst, J. D. and Krasnogor, N.},
    year = 2008,
    doi = {10.1093/bioinformatics/btn050},
    month = apr,
    journal = {Bioinformatics},
    volume = {24},
    number = {7},
    pages = {916--923}
  }