A parallel version of the branch & prune algorithm for the molecular distance geometry problem

2010 ACS/IEEE International Conference on Computer Systems and Applications, AICCSA 2010

Volumn , Issue , 2010, Pages

  Mucherino, A ^a   Lavor, C ^b   Liberti, L ^c   Talbi, E G ^a  

^a INRIA   (France)

^b UNIVERSITY OF CAMPINAS   (Brazil)

^c ÉCOLE POLYTECHNIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HEURISTIC ALGORITHMS;

BP ALGORITHM; COMPUTATIONAL EXPERIMENT; GRID INFRASTRUCTURES; META HEURISTIC ALGORITHM; MOLECULAR DISTANCE GEOMETRY PROBLEM; NUCLEAR MAGNETIC RESONANCE (NMR); PARALLEL VERSION;

NUCLEAR MAGNETIC RESONANCE;

EID: 78049478753     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/AICCSA.2010.5586983     Document Type: Conference Paper

References (18)

1. B. Berger, J. Kleinberg and T. Leighton, Reconstructing a Three-Dimensional Model with Arbitrary Errors, Journal of the ACM 46, 212-235, 1999.
2. P. Biswas, K.-C. Toh, and Y. Ye, A Distributed SDP Approach for Large-Scale Noisy Anchor-Free Graph Realization with Applications to Molecular Coriformation, SIAM Journal on Scientific Computing 30, 1251-1277, 2008.
3. R. Bolze, F. Cappello, E. aron, M. Daydé, F. Desprez, E. Jeannot, Y. Jégou, S. Lantéri, J. Leduc, N. Melab, G. Mornet, R. Namyst, P. Primet, B. Quetier, O. Richard, E-G. Talbi and I. Touche, Grid'5000: a Large Scale and Highly Reconfigurable Experimental Grid Testbed, International Journal of High Performance Computing Applications 20 (4), 481-494, 2006.
4. G.M. Crippen and T.F. Havel, Distance Geometry and Molecular Conformation, John Wiley & Sons, New York, 1988.
5. W. Gronwald, H.R. Kalbitzer, Automated Structure Determination of Proteins by NMR Spectroscopy, Progress in Nuclear Magnetic Resonance Spectroscopy 44 (1-2), 33-96, 2004.
6. W.D. Gropp, Ewing Lusk, User's Guide for mpich, a Portable Implementation of MPI, Mathematics and Computer Science Division, Argonne National Laboratory, 1996.
7. W. Gropp, E. Lusk, N. Doss, A. Skjellum, A High-Performance, Portable Implementation of the MPI Message Passing Interface Standard, Parallel Computing 22 (6), 789-828, 1996.
8. A. Grosso, M. Locatelli, F. Schoen, Solving Molecular Distance Geometry Problems by Global Optimization Algorithms, Computational Optimization and Applications 43, 23-27, 2009.
9. T.F. Havel, Distance Geometry, In: D.M. Grant and R.K. Harris (Eds.), Encyclopedia of Nuclear Magnetic Resonance, Wiley, New York, 1701-1710, 1995.
10. C. Lavor, On Generating Instances for the Molecular Distance Geometry Problem, In: L. Liberti and N. Maculan (Eds.), Global Optimization: from Theory to Implementation, Springer, New York, 405-414, 2006.
11. C. Lavor, L. Liberti, and N. Maculan, Discretizable Molecular Distance Geometry Problem, Tech. Rep. q-bio.BM/0608012, arXiv, 2006.
12. nd edition, Springer, New York, 2305-2311, 2009.
13. L. Liberti, C. Lavor, and N. Maculan, A Branch-and-Prune Algorithm for the Molecular Distance Geometry Problem, International Transactions in Operational Research 15 (1), 1-17, 2008.
14. L. Liberti, C. Lavor, A. Mucherino, N. Maculan, Molecular Distance Geometry Methods: from Continuous to Discrete, to appear in International Transactions in Operational Research, 2010.
15. lJ. Moré, Z. Wu, Global Continuation for Distance Geometry Problems, SIAM Journal on Optimization 7, 814-836, 1997.
16. A. Mucherino, L. Liberti, C. Lavor, and N. Maculan, Comparisons between an Exact and a MetaHeuristic Algorithm for the Molecular Distance Geometry Problem, ACM Conference Proceedings, Genetic and Evolutionary Computation Conference (GECCO09), Montreal, Canada, 333-340, 2009.
17. th Allerton Conference in Communications, Control, and Computing, Monticello, IL, 480-489, 1979.
18. T. Schlick, Molecular Modelling and Simulation: an Interdisciplinary Guide, Springer, New York, 2002.