A parallel BP algorithm for the discretizable distance geometry problem

Proceedings of the 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2012

Volumn , Issue , 2012, Pages 1762-1768

  Gramacho, W ^a   Mucherino, A ^b   Lavor, C ^c   Maculan, N ^d  

^a UNIVERSIDADE FEDERAL DO TOCANTINS   (Brazil)

^b UNIVERSITÉ DE RENNES 1   (France)

^c UNIVERSITY OF CAMPINAS   (Brazil)

^d FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

branch and prune; discretization; distance geometry; parallel computing

Indexed keywords

BP ALGORITHM; BRANCH-AND-PRUNE; COMMON COORDINATE SYSTEMS; COMPUTATIONAL EXPERIMENT; DISCRETIZATIONS; DISTANCE GEOMETRY; PARALLEL VERSION; VERTEX SET;

DISTRIBUTED PARAMETER NETWORKS; GEOMETRY; PARALLEL ALGORITHMS; PARALLEL ARCHITECTURES;

PARALLEL PROCESSING SYSTEMS;

EID: 84867435730     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPSW.2012.218     Document Type: Conference Paper

References (30)

1. D. Aloise, S. Cafieri, G. Caporossi, P. Hansen, L. Liberti, S. Perron, Column Generation Algorithms for Exact Modularity Maximization in Networks, Physical Review E 82:046112, 2010.
2. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne, The Protein Data Bank, Nucleic Acids Research 28, 235-242, 2000.
3. P. Biswas, K.C. Toh, and Y. Ye, A distributed SDP Approach for Large-Scale Noisy Anchor-Free Graph Realization with Applications to Molecular Conformation, SIAM Journal on Scientific Computing 30, 1251-1277, 2008.
4. S. Cafieri, P. Hansen, L. Liberti, Locally Optimal Heuristic for Modularity Maximization of Networks, Physical Review E 83:056105, 2011.
5. S. Cafieri, P. Hansen, L. Liberti, Loops and Multiple Edges in Modularity Maximization of Networks, Physical Review E 81:046102, 2010.
6. I.D. Coope, Reliable Computation of the Points of Intersection of n Spheres in n-space, ANZIAM Journal 42, 461-477, 2000.
7. G.M. Crippen and T.F. Havel, Distance Geometry and Molecular Conformation, John Wiley & Sons, New York, 1988.
8. Q. Dong and Z. Wu, A Geometric Build-Up Algorithm for Solving the Molecular Distance Geometry Problem with Sparse Distance Data, Journal of Global Optimization, 26, 321-333, 2003.
9. T.F. Havel, Distance Geometry, D.M. Grant and R.K. Harris (Eds.), Encyclopedia of Nuclear Magnetic Resonance, Wiley, New York, 1701-1710, 1995.
10. N. Krislock, H. Wolkowicz, Explicit Sensor Network Localization using Semidefinite Representations and Facial Reductions, SIAM Journal on Optimization 20, 2679-2708, 2010.
11. C. Lavor, J. Lee, A. Lee-St.John, L. Liberti, A. Mucherino, M. Sviridenko, Discretization Orders for Distance Geometry Problems, to appear in Optimization Letters, 2012.
12. C. Lavor, L. Liberti, N. Maculan, A. Mucherino, The Discretizable Molecular Distance Geometry Problem, to appear in Computational Optimization and Applications, 2012.
13. C. Lavor, L. Liberti, N. Maculan, A. Mucherino, Recent Advances on the Discretizable Molecular Distance Geometry Problem, European Journal of Operational Research 219, 698-706, 2012.
14. C. Lavor, L. Liberti, A. Mucherino, On the Solution of Molecular Distance Geometry Problems with Interval Data, IEEE Conference Proceedings, International Workshop on Computational Proteomics, International Conference on Bioinformatics & Biomedicine (BIBM10), Hong Kong, 77-82, 2010.
15. C. Lavor, L. Liberti, A. Mucherino, The interval Branch-and-Prune Algorithm for the Discretizable Molecular Distance Geometry Problem with Inexact Distances, to appear in Journal of Global Optimization, 2012.
16. th Annual ACM Symposium on Applied Computing, Hawaii, USA, 804-805, 2009.
17. C. Lavor, A. Mucherino, L. Liberti, N. Maculan, On the Computation of Protein Backbones by using Artificial Backbones of Hydrogens, Journal of Global Optimization, 50, 329-344, 2011.
18. L. Liberti, C. Lavor, and N. Maculan, A Branch-and-Prune Algorithm for the Molecular Distance Geometry Problem, International Transactions in Operational Research 15, 1-17, 2008.
19. th International Symposium on Bioinformatics Research and Applications (ISBRA11), Changsha, China, May 2011.
20. L. Liberti, C. Lavor, A. Mucherino, N. Maculan, Molecular Distance Geometry Methods: from Continuous to Discrete, International Transactions in Operational Research 18, 33-51, 2010.
21. th Cologne-Twente Workshop on Graphs and Combinatorial Optimization (CTW11), Rome, Italy, 189-193, 2011.
22. th Annual International Conference on Combinatorial Optimization and Applications (COCOA11), Zhangjiajie, China, 322-342, 2011.
23. A. Noack, R. Rotta, Multi-level Algorithms for Modularity Clustering, Lecture Notes in Computer Science 5526, 257-268, 2009.
24. A. Mucherino, C. Lavor, L. Liberti, The Discretizable Distance Geometry Problem, to appear in Optimization Letters, 2012.
25. A. Mucherino, C. Lavor, L. Liberti, E-G. Talbi, A Parallel Version of the Branch & Prune Algorithm for the Molecular Distance Geometry Problem, IEEE Conference Proceedings, ACS/IEEE International Conference on Computer Systems and Applications (AICCSA10), Hammamet, Tunisia, 1-6, 2010.
26. A. Mucherino, C. Lavor, T. Malliavin, L. Liberti, M. Nilges, M. Maculan, Influence of Pruning Devices on the Solution of Molecular Distance Geometry Problems, Lecture Notes in Computer Science 6630, P.M. Pardalos and S. Rebennack (Eds.), Proceedings of the 10th International Symposium on Experimental Algorithms (SEA11), Crete, Greece, 206-217, 2011.
27. A. Mucherino, L. Liberti, C. Lavor, MD-jeep: an Implementation of a Branch & Prune Algorithm for Distance Geometry Problems, Lectures Notes in Computer Science 6327, K. Fukuda et al. (Eds.), Proceedings of the Third International Congress on Mathematical Software (ICMS10), Kobe, Japan, 186-197, 2010.
28. M. Nilges, A.M. Gronenborn, A.T. Brunger, G.M. Clore, Determination of Three-Dimensional Structures of Proteins by Simulated Annealing with Interproton Distance Restraints. Application to Crambin, Potato Carboxypeptidase Inhibitor and Barley Serine Proteinase Inhibitor 2, Protein Engineering 2, 27-38, 1988.
29. th Allerton Conference in Communications, Control and Computing, 480-489, 1979.
30. D. Wu, Z. Wu, Y. Yuan, Rigid Versus Unique Determination of Protein Structures with Geometric Buildup, Optimization Letters 2, 319-331, 2008.