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Heuristics, optimizations, and parallelism for protein structure prediction in CLP(FD)

Published: 11 July 2005 Publication History

Abstract

The paper describes a constraint-based solution to the protein folding problem on face-centered cubic lattices---a biologically meaningful approximation of the general protein folding problem. The paper improves the results presented in [15] and introduces new ideas for improving efficiency: (i) proper reorganization of the constraint structure; (ii) development of novel, both general and problem-specific, heuristics; (iii) exploitation of parallelism. Globally, we obtain a speed up in the order of 60 w.r.t. [15]. We show how these results can be employed to solve the folding problem for large proteins containing subsequences whose conformation is already known.

References

[1]
R. Agarwala et al. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. J. of Computational Biology, pages 275--296, 1997.
[2]
K. R. Apt. Principles of constraint programming. Cambridge University press, 2003.
[3]
R. Backofen. The protein structure prediction problem: A constraint optimization approach using a new lower bound. Constraints, 6(2--3):223--255, 2001.
[4]
R. Backofen and S. Will. Fast, constraint-based threading of HP sequences to hydrophobic cores. Int. Conf. on Principle and Practice of Constraint Programming, 494--508, 2001. Springer Verlag.
[5]
R. Backofen and S. Will. A Constraint-Based Approach to Structure Prediction for Simplified Protein Models that Outperforms Other Existing Methods. ICLP, 2003, Springer Verlag.
[6]
H. M. Berman et al. The protein data bank. Nucleic Acids Research, 28:235--242, 2000. http://www.rcsb.org/pdb/.
[7]
M. Berrera, H. Molinari, and F. Fogolari. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics, 4(8), 2003.
[8]
R. Bonneau and D. Baker. Ab initio protein structure prediction: progress and prospects. Annu. Rev. Biophys. Biomol. Struct., 30:173--89, 2001.
[9]
B. R. Brooks et al. Charmm: A program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem., 4:187--217, 1983.
[10]
M. Carlsson, G. Ottosson, and B. Carlson. An open-ended finite domain constraint solver. PLILP, Springer Verlag, 1997.
[11]
A. M. Cheadle et al. ECLiPSe: An Introduction. Technical Report IC-Parc 03--1, IC-Parc, 2003.
[12]
D. Clark, J. Shirazi, and C. Rawlings. Protein topology prediction through constraint-based search and the evaluation of topological folding rules. Protein Engineering, 4:752--760, 1991.
[13]
P. Clote and R. Backofen. Computational Molecular Biology: An Introduction. John Wiley & Sons, 2001.
[14]
P. Crescenzi et al. On the complexity of protein folding. In Proc. of STOC, pages 597--603, 1998.
[15]
A. Dal Palù, A. Dovier, and F. Fogolari. Constraint logic programming approach to protein structure prediction. BMC Bioinformatics, 5(186), 2004.
[16]
A. Dal Palù, A. Dovier, and F. Fogolari. Protein folding in CLP(FD) with empirical contact energies. In Recent Advances in Constraints, Springer Verlag, 2004.
[17]
F. Fogolari et al. Modeling of polypeptide chains as C-α chains, C-α chains with C-β, and C-α chains with ellipsoidal lateral chains. Biophysical Journal, 70:1183--1197, 1996.
[18]
S. Forman. Torsion Angle Selection and Emergent Non-local Secondary Structure in Protein Structure Prediction. PhD thesis, U. of Iowa, 2001.
[19]
G. Gupta, E. Pontelli, M. Carlsson, M. Hermegildo, K. Ali. Parallel Execution of Prolog: a Survey. ACM TOPLAS, 23(4):472--602, 2001.
[20]
W. Hart and S. Israil. Fast protein folding in the hydrophobic-hytrophilic model within three-eighths of optimal. J. of Computational Biology, pages 53--96, 1996.
[21]
S. Miyazawa and R. L. Jernigan. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. of Molecular Biology, 256(3):623--644, 1996.
[22]
A. Newman. A New Algorithm for Protein Folding in the HP Model. In Symposium on Discrete Algorithms. Springer Verlag, 2002.
[23]
Committee on Mathematical Challenges from Computational Chemistry. National Research Council, 1995.
[24]
D. Qiu, P. Shenkin, F. Hollinger, and W. Still. The gb/sa continuum model for solvation. A fast analytical method for the calculation of approximate born radii. J. Phys. Chem., 101:3005--3014, 1997.
[25]
G. Raghunathan and R. L. Jernigan. Ideal architecture of residue packing and its observation in protein structures. Protein Science, 6:2072--2083, 1997.
[26]
B. Rost and C. Sander. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232:584--599, 1993.
[27]
K. Simons et al. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 1999, 3:171--176.
[28]
J. Skolnick and A. Kolinski. Computational studies of protein folding. Computing in Science and Engineering, 3(5):40--50, 2001.
[29]
J. Skolnick and A. Kolinski. Reduced models of proteins and their applications. Polymer, 45:511--524, 2004.
[30]
Swedish Institute for Computer Science. Sicstus Prolog. http://www.sics.se/sicstus/.
[31]
L. Toma and S. Toma. Folding simulation of protein models on the structure-based cubo-octahedral lattice with contact interactions algorithm. Protein Science, 8:196--202, 1999.
[32]
M.L.G. William and D. Harvey. Limited discrepancy search. IJCAI, pages 607--615, Morgan Kaufmann, 1995.

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  • (2023)Protein Folding Optimization Using Butterfly Optimization AlgorithmMachine Intelligence and Emerging Technologies10.1007/978-3-031-34622-4_61(775-787)Online publication date: 11-Jun-2023
  • (2015) Efficient conformational space exploration in ab initio protein folding simulation Royal Society Open Science10.1098/rsos.1502382:8(150238)Online publication date: Aug-2015
  • (2014)Constraint-Based Evolutionary Local Search for Protein Structures with Secondary MotifsPRICAI 2014: Trends in Artificial Intelligence10.1007/978-3-319-13560-1_27(333-344)Online publication date: 2014
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    cover image ACM Conferences
    PPDP '05: Proceedings of the 7th ACM SIGPLAN international conference on Principles and practice of declarative programming
    July 2005
    260 pages
    ISBN:1595930906
    DOI:10.1145/1069774
    • General Chair:
    • Pedro Barahona,
    • Program Chair:
    • Amy Felty
    Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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    Published: 11 July 2005

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    Author Tags

    1. bioinformatics
    2. constraint logic programming
    3. parallelism

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    View all
    • (2023)Protein Folding Optimization Using Butterfly Optimization AlgorithmMachine Intelligence and Emerging Technologies10.1007/978-3-031-34622-4_61(775-787)Online publication date: 11-Jun-2023
    • (2015) Efficient conformational space exploration in ab initio protein folding simulation Royal Society Open Science10.1098/rsos.1502382:8(150238)Online publication date: Aug-2015
    • (2014)Constraint-Based Evolutionary Local Search for Protein Structures with Secondary MotifsPRICAI 2014: Trends in Artificial Intelligence10.1007/978-3-319-13560-1_27(333-344)Online publication date: 2014
    • (2013)Neighborhood Selection in Constraint-Based Local Search for Protein Structure PredictionProceedings of the 26th Australasian Joint Conference on AI 2013: Advances in Artificial Intelligence - Volume 827210.1007/978-3-319-03680-9_5(44-55)Online publication date: 1-Dec-2013
    • (2010)25 years of applications of logic programming in ItalyA 25-year perspective on logic programming10.5555/1880413.1880428(300-328)Online publication date: 1-Jan-2010
    • (2010)25 Years of Applications of Logic Programming in ItalyA 25-Year Perspective on Logic Programming10.1007/978-3-642-14309-0_14(300-328)Online publication date: 2010
    • (2009)Logic Programming Techniques in Protein Structure DeterminationProceedings of the 10th International Conference on Logic Programming and Nonmonotonic Reasoning10.1007/978-3-642-04238-6_58(560-566)Online publication date: 1-Sep-2009
    • (2007)A constraint solver for discrete lattices, its parallelization, and application to protein structure predictionSoftware: Practice and Experience10.1002/spe.81037:13(1405-1449)Online publication date: 12-Mar-2007
    • (2005)Specification and verification of agent interaction using abductive reasoningProceedings of the 6th international conference on Computational Logic in Multi-Agent Systems10.1007/11750734_14(243-264)Online publication date: 27-Jun-2005
    • (2005)A new constraint solver for 3d lattices and its application to the protein folding problemProceedings of the 12th international conference on Logic for Programming, Artificial Intelligence, and Reasoning10.1007/11591191_5(48-63)Online publication date: 2-Dec-2005

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