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Volumn 18, Issue 1, 2011, Pages 33-51

Molecular distance geometry methods: From continuous to discrete

Author keywords

Distance geometry; Optimization; Protein conformation

Indexed keywords

DISCRETE METHOD; DISCRETE SETS; DISTANCE GEOMETRY; EUCLIDEAN; EUCLIDEAN SPACES; GRAPH DRAWING; K-SPACE; MOLECULAR DISTANCES; POWER-LOSSES; PROBLEM STRUCTURE; PROTEIN CONFORMATION; RELATIVE DISTANCES; SENSOR NETWORK LOCALIZATION; THREE DIMENSIONS; WIRELESS SENSOR;

EID: 84863430641     PISSN: 09696016     EISSN: 14753995     Source Type: Journal    
DOI: 10.1111/j.1475-3995.2009.00757.x     Document Type: Article
Times cited : (99)

References (56)
  • 1
    • 63149188884 scopus 로고    scopus 로고
    • Localization in sensor networks
    • Stojmenović, I. (ed.) Wiley, Chichester
    • Bachrach, J., Taylor, C., 2005. Localization in sensor networks. In Stojmenović, I. (ed.) Handbook of Sensor Networks. Wiley, Chichester, pp. 3627-3643.
    • (2005) Handbook of Sensor Networks , pp. 3627-3643
    • Bachrach, J.1    Taylor, C.2
  • 4
    • 55549138762 scopus 로고    scopus 로고
    • A distributed SDP approach for large-scale noisy anchor-free graph realization with applications to molecular conformation
    • Biswas, P., Toh, K.C., Ye, Y., 2008. A distributed SDP approach for large-scale noisy anchor-free graph realization with applications to molecular conformation. SIAM Journal on Scientific Computing 30, 3, 1251-1277.
    • (2008) SIAM Journal on Scientific Computing , vol.30 , Issue.3 , pp. 1251-1277
    • Biswas, P.1    Toh, K.C.2    Ye, Y.3
  • 5
    • 52049122134 scopus 로고    scopus 로고
    • Extending the geometric build-up algorithm for the molecular distance geometry problem
    • Carvalho, R.S., Lavor, C., Protti, F., 2008. Extending the geometric build-up algorithm for the molecular distance geometry problem. Information Processing Letters 108, 234-237.
    • (2008) Information Processing Letters , vol.108 , pp. 234-237
    • Carvalho, R.S.1    Lavor, C.2    Protti, F.3
  • 6
    • 0027680673 scopus 로고
    • Isotropic effective energy simulated annealing searches for low energy molecular cluster states
    • Coleman, T.F., Shalloway, D., Wu, Z., 1993. Isotropic effective energy simulated annealing searches for low energy molecular cluster states. Computational Optimization and Applications 2, 145-170.
    • (1993) Computational Optimization and Applications , vol.2 , pp. 145-170
    • Coleman, T.F.1    Shalloway, D.2    Wu, Z.3
  • 7
    • 0000999426 scopus 로고
    • A parallel build-up algorithm for global energy minimizations of molecular clusters using effective energy simulated annealing
    • Coleman, T.F., Shalloway, D., Wu, Z., 1994. A parallel build-up algorithm for global energy minimizations of molecular clusters using effective energy simulated annealing. Journal of Global Optimization 4, 171-185.
    • (1994) Journal of Global Optimization , vol.4 , pp. 171-185
    • Coleman, T.F.1    Shalloway, D.2    Wu, Z.3
  • 9
    • 31244436296 scopus 로고    scopus 로고
    • A linear-time algorithm for solving the molecular distance geometry problem with exact interatomic distances
    • Dong, Q., Wu, Z., 2002. A linear-time algorithm for solving the molecular distance geometry problem with exact interatomic distances. Journal of Global Optimization 22, 365-375.
    • (2002) Journal of Global Optimization , vol.22 , pp. 365-375
    • Dong, Q.1    Wu, Z.2
  • 10
    • 84867962761 scopus 로고    scopus 로고
    • A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
    • Dong, Q., Wu, Z., 2003. A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data. Journal of Global Optimization 26, 321-333.
    • (2003) Journal of Global Optimization , vol.26 , pp. 321-333
    • Dong, Q.1    Wu, Z.2
  • 12
    • 0001114105 scopus 로고
    • Almost all simply connected closed surfaces are rigid
    • Dold, A., Eckmann, B. (eds) Springer, Berlin
    • Gluck, H., 1975. Almost all simply connected closed surfaces are rigid. In Dold, A., Eckmann, B. (eds) Geometric Topology, Volume 438 of Lecture Notes in Mathematics. Springer, Berlin, pp. 225-239.
    • (1975) Geometric Topology, Volume 438 of Lecture Notes in Mathematics , pp. 225-239
    • Gluck, H.1
  • 13
    • 0000771519 scopus 로고
    • An alternating projection algorithm for computing the nearest Euclidean distance matrix
    • Glunt, W., Hayden, T.H., Hong, S., Wells, J., 1990. An alternating projection algorithm for computing the nearest Euclidean distance matrix. SIAM Journal on Matrix Analysis and Applications 11, 4, 589-600.
    • (1990) SIAM Journal on Matrix Analysis and Applications , vol.11 , Issue.4 , pp. 589-600
    • Glunt, W.1    Hayden, T.H.2    Hong, S.3    Wells, J.4
  • 16
    • 0026821495 scopus 로고
    • Conditions for unique graph realizations
    • Hendrickson, B.A., 1992. Conditions for unique graph realizations. SIAM Journal on Computing 21, 1, 65-84.
    • (1992) SIAM Journal on Computing , vol.21 , Issue.1 , pp. 65-84
    • Hendrickson, B.A.1
  • 17
    • 0013558430 scopus 로고
    • The molecule problem: Exploiting structure in global optimization
    • Hendrickson, B.A., 1995. The molecule problem: Exploiting structure in global optimization. SIAM Journal on Optimization 5, 835-857.
    • (1995) SIAM Journal on Optimization , vol.5 , pp. 835-857
    • Hendrickson, B.A.1
  • 18
    • 0242485191 scopus 로고    scopus 로고
    • Solving large scale molecular distance geometry problems by a smoothing technique via the gaussian transform and d.c. programming
    • Hoai An, L.T., 2003. Solving large scale molecular distance geometry problems by a smoothing technique via the gaussian transform and d.c. programming. Journal of Global Optimization 27, 375-397.
    • (2003) Journal of Global Optimization , vol.27 , pp. 375-397
    • Hoai An, L.T.1
  • 19
    • 1542380919 scopus 로고    scopus 로고
    • Large-scale molecular optimization from distance matrices by a d.c. optimization approach
    • Hoai An, L.T., Tao, P.D., 2003. Large-scale molecular optimization from distance matrices by a d.c. optimization approach. SIAM Journal on Optimization 14, 77-114.
    • (2003) SIAM Journal on Optimization , vol.14 , pp. 77-114
    • Hoai An, L.T.1    Tao, P.D.2
  • 20
    • 33751234960 scopus 로고    scopus 로고
    • A distance geometry heuristic for expanding the range of geometries sampled during conformational search
    • Izrailev, S., Zhu, F., Agrafiotis, D.K., 2006. A distance geometry heuristic for expanding the range of geometries sampled during conformational search. Journal of Computational Chemistry 26, 3, 1962-1969.
    • (2006) Journal of Computational Chemistry , vol.26 , Issue.3 , pp. 1962-1969
    • Izrailev, S.1    Zhu, F.2    Agrafiotis, D.K.3
  • 21
    • 0026156982 scopus 로고
    • Diffusion equation method of global minimization: Performance for standard functions
    • Kostrowicki, J., Piela, L., 1991. Diffusion equation method of global minimization: Performance for standard functions. Journal of Optimization Theory and Applications 69, 269-284.
    • (1991) Journal of Optimization Theory and Applications , vol.69 , pp. 269-284
    • Kostrowicki, J.1    Piela, L.2
  • 22
    • 0001425721 scopus 로고
    • Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms
    • Kostrowicki, J., Piela, L., Cherayil, B.J., Scheraga, H.A., 1991. Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms. Journal of Physical Chemistry 95, 4113-4119.
    • (1991) Journal of Physical Chemistry , vol.95 , pp. 4113-4119
    • Kostrowicki, J.1    Piela, L.2    Cherayil, B.J.3    Scheraga, H.A.4
  • 23
    • 0001031118 scopus 로고
    • Application of the diffusion equation method for global optimization of oligopeptides
    • Kostrowicki, J., Scheraga, H.A., 1992. Application of the diffusion equation method for global optimization of oligopeptides. Journal of Physical Chemistry 96, 7442-7449.
    • (1992) Journal of Physical Chemistry , vol.96 , pp. 7442-7449
    • Kostrowicki, J.1    Scheraga, H.A.2
  • 24
    • 24044443193 scopus 로고    scopus 로고
    • Application of deterministic low-discrepancy sequences in global optimization
    • Kucherenko, S., Sytsko, Yu., 2004. Application of deterministic low-discrepancy sequences in global optimization. Computational Optimization and Applications 30, 3, 297-318.
    • (2004) Computational Optimization and Applications , vol.30 , Issue.3 , pp. 297-318
    • Kucherenko, S.1    Sytsko, Y.2
  • 25
    • 72949101175 scopus 로고    scopus 로고
    • On generating instances for the molecular distance geometry problem
    • Liberti, L., Maculan, N. (eds) Springer, Berlin
    • Lavor, C., 2006. On generating instances for the molecular distance geometry problem. In Liberti, L., Maculan, N. (eds) Global Optimization: From Theory to Implementation. Springer, Berlin, pp. 405-414.
    • (2006) Global Optimization: From Theory to Implementation , pp. 405-414
    • Lavor, C.1
  • 26
    • 59449086627 scopus 로고    scopus 로고
    • Computational experience with the molecular distance geometry problem
    • Pinté r, J. (ed.) Springer, Berlin
    • Lavor, C., Liberti, L., Maculan, N., 2006. Computational experience with the molecular distance geometry problem. In Pinté r, J. (ed.) Global Optimization: Scientific and Engineering Case Studies. Springer, Berlin, pp. 213-225.
    • (2006) Global Optimization: Scientific and Engineering Case Studies , pp. 213-225
    • Lavor, C.1    Liberti, L.2    Maculan, N.3
  • 27
    • 72749085157 scopus 로고    scopus 로고
    • Molecular distance geometry problem
    • Floudas, C., Pardalos, P. (eds) (2nd edn), Springer, New York
    • Lavor, C., Liberti, L., Maculan, N., 2009a. Molecular distance geometry problem. In Floudas, C., Pardalos, P. (eds) Encyclopedia of Optimization, (2nd edn), Springer, New York, pp. 2305-2311.
    • (2009) Encyclopedia of Optimization , pp. 2305-2311
    • Lavor, C.1    Liberti, L.2    Maculan, N.3
  • 30
    • 61549115200 scopus 로고    scopus 로고
    • Writing global optimization software
    • Liberti, L., Maculan, N. (eds) Springer, Berlin
    • Liberti, L., 2006. Writing global optimization software. In Liberti, L., Maculan, N. (eds) Global Optimization: From Theory to Implementation. Springer, Berlin, pp. 211-262.
    • (2006) Global Optimization: From Theory to Implementation , pp. 211-262
    • Liberti, L.1
  • 31
    • 44649162530 scopus 로고    scopus 로고
    • Variable neighbourhood search for the global optimization of constrained NLPs
    • Workshop, Almeria, Spain
    • Liberti, L., Dražic, M., 2005. Variable neighbourhood search for the global optimization of constrained NLPs. In Proceedings of GO, Workshop, Almeria, Spain.
    • (2005) Proceedings of GO
    • Liberti, L.1    Dražic, M.2
  • 34
    • 59449085654 scopus 로고    scopus 로고
    • Double variable neighbourhood search with smoothing for the molecular distance geometry problem
    • Liberti, L., Lavor, C., Maculan, N., Marinelli, F., 2009a. Double variable neighbourhood search with smoothing for the molecular distance geometry problem. Journal of Global Optimization 43, 207-218.
    • (2009) Journal of Global Optimization , vol.43 , pp. 207-218
    • Liberti, L.1    Lavor, C.2    Maculan, N.3    Marinelli, F.4
  • 38
    • 0031285908 scopus 로고    scopus 로고
    • Global continuation for distance geometry problems
    • Moré, J.J., Wu, Z., 1997. Global continuation for distance geometry problems. SIAM Journal on Optimization 7, 3, 814-846.
    • (1997) SIAM Journal on Optimization , vol.7 , Issue.3 , pp. 814-846
    • Moré, J.J.1    Wu, Z.2
  • 39
    • 78149241977 scopus 로고    scopus 로고
    • The branch and prune algorithm for the molecular distance geometry problem with inexact distances
    • World Academy of Science, Engineering and Technology
    • Mucherino, A., Lavor, C., 2009. The branch and prune algorithm for the molecular distance geometry problem with inexact distances. In Proceedings of the International Conference on Computational Biology, Vol. 58. World Academy of Science, Engineering and Technology, pp. 349-353.
    • (2009) Proceedings of the International Conference on Computational Biology , vol.58 , pp. 349-353
    • Mucherino, A.1    Lavor, C.2
  • 40
    • 79956223394 scopus 로고    scopus 로고
    • The molecular distance geometry problem applied to protein conformations
    • Cafieri S., Mucherino, A., Nannicini, G., Tarissan, F., Liberti, L. (eds) É cole Polytechnique, Paris
    • Mucherino, A., Lavor, C., Maculan, N., 2009a. The molecular distance geometry problem applied to protein conformations. In Cafieri, S., Mucherino, A., Nannicini, G., Tarissan, F., Liberti, L. (eds) Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization. É cole Polytechnique, Paris, pp. 337-340.
    • (2009) Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization , pp. 337-340
    • Mucherino, A.1    Lavor, C.2    Maculan, N.3
  • 41
    • 72749092411 scopus 로고    scopus 로고
    • Comparisons between an exact and a metaheuristic algorithm for the molecular distance geometry problem
    • Rothlauf, F. (ed.) ACM, Montreal
    • Mucherino, A., Liberti, L., Lavor, C., Maculan, N., 2009b. Comparisons between an exact and a metaheuristic algorithm for the molecular distance geometry problem. In Rothlauf, F. (ed.) Proceedings of the Genetic and Evolutionary Computation Conference. ACM, Montreal, pp. 333-340.
    • (2009) Proceedings of the Genetic and Evolutionary Computation Conference , pp. 333-340
    • Mucherino, A.1    Liberti, L.2    Lavor, C.3    Maculan, N.4
  • 42
    • 0000594925 scopus 로고
    • The multiple-minima problem in the conformational analysis of molecules: Deformation of the protein energy hypersurface by the diffusion equation method
    • Piela, L., Kostrowicki, J., Scheraga, H.A., 1989. The multiple-minima problem in the conformational analysis of molecules: Deformation of the protein energy hypersurface by the diffusion equation method. Journal of Physical Chemistry 93, 3339-3346.
    • (1989) Journal of Physical Chemistry , vol.93 , pp. 3339-3346
    • Piela, L.1    Kostrowicki, J.2    Scheraga, H.A.3
  • 44
    • 0003167703 scopus 로고
    • Rigid and flexible frameworks
    • Roth, B., 1981. Rigid and flexible frameworks. American Mathematical Monthly 88, 1, 6-21.
    • (1981) American Mathematical Monthly , vol.88 , Issue.1 , pp. 6-21
    • Roth, B.1
  • 45
    • 84857915033 scopus 로고    scopus 로고
    • Combining variable neighbourhood search and estimation of distribution algorithms in the protein side chain placement problem
    • Tenerife, Spain
    • Santana, R., Larrañaga, P., Lozano, J.A., 2005. Combining variable neighbourhood search and estimation of distribution algorithms in the protein side chain placement problem. In Proceedings of Mini Euro Conference on Variable Neighbourhood Search, Tenerife, Spain.
    • (2005) Proceedings of Mini Euro Conference on Variable Neighbourhood Search
    • Santana, R.1    Larrañaga, P.2    Lozano, J.A.3
  • 46
    • 51649105201 scopus 로고    scopus 로고
    • Combining variable neighbourhood search and estimation of distribution algorithms in the protein side chain placement problem
    • Santana, R., Larrañaga, P., Lozano, J.A., 2008. Combining variable neighbourhood search and estimation of distribution algorithms in the protein side chain placement problem. Journal of Heuristics 14, 519-547.
    • (2008) Journal of Heuristics , vol.14 , pp. 519-547
    • Santana, R.1    Larrañaga, P.2    Lozano, J.A.3
  • 47
    • 0002702652 scopus 로고
    • Embeddability of weighted graphs in k-space is strongly NP-hard
    • Control and Computing, Allerton
    • Saxe, J.B., 1979. Embeddability of weighted graphs in k-space is strongly NP-hard. Proceedings of 17th Allerton Conference in Communications, Control and Computing, Allerton, pp. 480-489.
    • (1979) Proceedings of 17th Allerton Conference in Communications , pp. 480-489
    • Saxe, J.B.1
  • 48
    • 0001203499 scopus 로고
    • Remarks to Maurice Fréchet's article "Sur la définition axiomatique d'une classe d'espaces distancié s vectoriellement applicabv sur l'espace de hilbert'
    • Schoenberg, I.J., 1935. Remarks to Maurice Fréchet's article "Sur la définition axiomatique d'une classe d'espaces distancié s vectoriellement applicable sur l'espace de hilbert". Annals of Mathematics 36, 3, 724-732.
    • (1935) Annals of Mathematics , vol.36 , Issue.3 , pp. 724-732
    • Schoenberg, I.J.1
  • 49
    • 0033134718 scopus 로고    scopus 로고
    • A symbolic reformulation/spatial branch-and-bound algorithm for the global optimisation of nonconvex MINLPs
    • Smith, E.M.B., Pantelides, C.C., 1999. A symbolic reformulation/spatial branch-and-bound algorithm for the global optimisation of nonconvex MINLPs. Computers and Chemical Engineering 23, 457-478.
    • (1999) Computers and Chemical Engineering , vol.23 , pp. 457-478
    • Smith, E.M.B.1    Pantelides, C.C.2
  • 50
    • 33846661142 scopus 로고    scopus 로고
    • Theory of semidefinite programming for sensor network localization
    • So, M.-C., Ye, Y., 2007. Theory of semidefinite programming for sensor network localization. Mathematical Programming 109, 367-384.
    • (2007) Mathematical Programming , vol.109 , pp. 367-384
    • So, M.-C.1    Ye, Y.2
  • 51
    • 2942665751 scopus 로고    scopus 로고
    • Global optimization of mixed integer nonlinear programs: A theoretical and computational study
    • Tawarmalani, M., Sahinidis, N.V., 2004. Global optimization of mixed integer nonlinear programs: A theoretical and computational study. Mathematical Programming 99, 563-591.
    • (2004) Mathematical Programming , vol.99 , pp. 563-591
    • Tawarmalani, M.1    Sahinidis, N.V.2
  • 52
    • 0035156982 scopus 로고    scopus 로고
    • Constrained global optimization for estimating molecular structure from atomic distances
    • Williams, G.A., Dugan, J.M., Altman, R.P., 2001. Constrained global optimization for estimating molecular structure from atomic distances. Journal of Computational Biology 8, 523-547.
    • (2001) Journal of Computational Biology , vol.8 , pp. 523-547
    • Williams, G.A.1    Dugan, J.M.2    Altman, R.P.3
  • 53
    • 33847251002 scopus 로고    scopus 로고
    • An updated geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
    • Wu, D., Wu, Z., 2007. An updated geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data. Journal of Global Optimization 37, 661-673.
    • (2007) Journal of Global Optimization , vol.37 , pp. 661-673
    • Wu, D.1    Wu, Z.2
  • 54
    • 43249103721 scopus 로고    scopus 로고
    • Rigid versus unique determination of protein structures with geometric buildup
    • Wu, D., Wu, Z., Yuan, Y., 2008. Rigid versus unique determination of protein structures with geometric buildup. Optimization Letters 2, 3, 319-331.
    • (2008) Optimization Letters , vol.2 , Issue.3 , pp. 319-331
    • Wu, D.1    Wu, Z.2    Yuan, Y.3
  • 55
    • 0030303861 scopus 로고    scopus 로고
    • The effective energy transformation scheme as a special continuation approach to global optimization with application to molecular conformation
    • Wu, Z., 1996. The effective energy transformation scheme as a special continuation approach to global optimization with application to molecular conformation. SIAM Journal on Optimization 6, 748-768.
    • (1996) SIAM Journal on Optimization , vol.6 , pp. 748-768
    • Wu, Z.1


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