CLP(FD) Approaches to the Protein Folding Problem

  1. A. Dovier, M. Burato, and F. Fogolari.
    Using Secondary Structure Information for Protein Folding in CLP(FD).
    In Proc. of Workshop on Functional and Constraint Logic Programming, ENTCS vol. 76, 2002.
    ( SICStus Prolog code, computational results on a PC Pentium 3, 500 MHz, and Some input Data, Sept. 5th, 2002)
  2. A. Dovier. Constraint Approach to the Protein Folding Problem.
    AI*IA Notizie, Volume 2, pp. 17-22, Giugno 2003.
  3. A. Dal Palù, A. Dovier, F. Fogolari.
    Protein Folding in CLP(FD) with Empirical Contact Energies.
    In Joint Annual Workshop of the ERCIM Working Group on Constraints and the CoLogNET area on Constraint and Logic Programming MTA SZTAKI, Budapest, Hungary 30 June - 2 July, 2003. LNCS Volume 3010, pages 250--265.
    ( SICStus Prolog code of the above paper, Potential Table, and Input Data, May, 5th, 2003)
  4. A. Dal Palu', S. Will, R. Backofen, and A. Dovier.
    Constraint Based Protein Structure Prediction Exploiting Secondary Structure Information (paper). In Proc. of CILC'04.
  5. A. Dal Palù, A. Dovier, and F. Fogolari.
    Constraint Logic Programming approach to protein structure prediction.
    BMC Bioinformatics 2004, 5:186, 30 November 2004.
    (Code and related files, June 2004)
  6. A. Dal Palù, A. Dovier, and E. Pontelli.
    Heuristics, Optimizations, and Parallelism for Protein Structure Prediction in CLP(FD).
    In Proc. of PPDP'05, Lisbon, 11-13 July 2005. ACM press, pp. 230-241 (also presented at CILC'05). (Code)
  7. A. Dal Palù, A.Dovier, and E. Pontelli.
    A New Constraint Solver for 3-D Lattices and its Application to the Protein Folding Problem.
    In proceedings of LPAR 2005, 2-6 Dec 2005, Montego Bay, Jamaica. (for the code, please email (dovier|dalpalu) at dimi.uniud.it )
  8. A. Dal Palu', A. Dovier, and E. Pontelli.
    A constraint solver for discrete lattices, its parallelization, and application to protein structure prediction. (draft)
    SOFTWARE-PRACTICE AND EXPERIENCE, 2007.
  9. A. Dovier, A. Dal Palù, E. Pontelli.
    Enhancing the Computation of Approximate Solutions of the Protein Structure Determination
    In Proceedings of the IEEE international conference on Bioinformatics and biomedicine workshops, 2-4 november 2007, fremont california, IEEE isbn 978-1-4244-1604-2 pp. 38-44.
  10. A. Dal Palù, A. Dovier, and E. Pontelli.
    Computing Approximate Solutions of the Protein Structure Determination Problem using Global Constraints on Discrete Crystal Lattices.
    Int'l Journal of Data Mining and Bioinformatics. 4(1):1-20. (draft and proofs as NMSU research report

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