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Volumn 95, Issue 10, 2008, Pages 4813-4819

Multiple sequence alignment by conformational space annealing

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Indexed keywords

PROTEIN;

EID: 58149279530     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.129684     Document Type: Article
Times cited : (33)

References (43)
  • 1
    • 0036208872 scopus 로고    scopus 로고
    • Recent progress in multiple sequence alignment: A survey
    • Notredame, C. 2002. Recent progress in multiple sequence alignment: a survey. Pharmacogenomics. 3:131-144.
    • (2002) Pharmacogenomics , vol.3 , pp. 131-144
    • Notredame, C.1
  • 2
    • 0024964655 scopus 로고
    • Gap costs for multiple sequence alignment
    • Altschul, S. F. 1989. Gap costs for multiple sequence alignment. J. Theor. Biol. 138:297-309.
    • (1989) J. Theor. Biol , vol.138 , pp. 297-309
    • Altschul, S.F.1
  • 4
    • 0031829993 scopus 로고    scopus 로고
    • COFFEE: An objective function for multiple sequence alignments
    • Notredame, C., L. Holm, and D. G. Higgins. 1998. COFFEE: an objective function for multiple sequence alignments. Bioinformatics. 14:407-422.
    • (1998) Bioinformatics , vol.14 , pp. 407-422
    • Notredame, C.1    Holm, L.2    Higgins, D.G.3
  • 5
    • 0028679709 scopus 로고
    • On the complexity of multiple sequence alignment
    • Wang, L., and T. Jiang. 1994. On the complexity of multiple sequence alignment. J. Comput. Biol. 1:337-348.
    • (1994) J. Comput. Biol , vol.1 , pp. 337-348
    • Wang, L.1    Jiang, T.2
  • 6
    • 0000303438 scopus 로고
    • The multiple sequence alignment problem in biology
    • Carrillo, H., and D. Lipman. 1988. The multiple sequence alignment problem in biology. SIAM J. Appl. Math. 48:1073-1082.
    • (1988) SIAM J. Appl. Math , vol.48 , pp. 1073-1082
    • Carrillo, H.1    Lipman, D.2
  • 7
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S. B., and C. D. Wunsch. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453.
    • (1970) J. Mol. Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 8
    • 0019887799 scopus 로고
    • Identification of common molecular sub sequences
    • Smith, T. F., and M. S. Waterman. 1981. Identification of common molecular sub sequences. J. Mol. Biol. 147:195-197.
    • (1981) J. Mol. Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 9
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng, D. F., and R. F. Doolittle. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25:351-360.
    • (1987) J. Mol. Evol , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 10
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 11
    • 0030582739 scopus 로고    scopus 로고
    • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
    • Gotoh, O. 1996. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol. 264:823-838.
    • (1996) J. Mol. Biol , vol.264 , pp. 823-838
    • Gotoh, O.1
  • 12
    • 0029861894 scopus 로고    scopus 로고
    • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    • Morgenstern, B., A. Dress, and T. Werner. 1996. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. USA. 93:12098-12103.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 12098-12103
    • Morgenstern, B.1    Dress, A.2    Werner, T.3
  • 13
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 14
    • 0034623005 scopus 로고    scopus 로고
    • T-COFFEE: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., D. G. Higgins, and J. Heringa. 2000. T-COFFEE: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
    • (2000) J. Mol. Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 15
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • Do, C. B., M. S. Mahabhashyam, M. Brudno, and S. Batzoglou. 2005. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res. 15:330-340.
    • (2005) Genome Res , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3    Batzoglou, S.4
  • 16
    • 24644512819 scopus 로고    scopus 로고
    • SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures
    • Zhou, H., and Y. Zhou. 2005. SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics. 21:3615-3621.
    • (2005) Bioinformatics , vol.21 , pp. 3615-3621
    • Zhou, H.1    Zhou, Y.2
  • 17
    • 11344292852 scopus 로고    scopus 로고
    • Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
    • Zhou, H., and Y. Zhou. 2005. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins. 58:321-328.
    • (2005) Proteins , vol.58 , pp. 321-328
    • Zhou, H.1    Zhou, Y.2
  • 18
    • 33750050261 scopus 로고    scopus 로고
    • A novel high resolution Calpha-Calpha distance dependent force field based on a high quality decoy set
    • Rajgaria, R., S. R. McAllister, and C. A. Floudas. 2006. A novel high resolution Calpha-Calpha distance dependent force field based on a high quality decoy set. Proteins. 65:726-741.
    • (2006) Proteins , vol.65 , pp. 726-741
    • Rajgaria, R.1    McAllister, S.R.2    Floudas, C.A.3
  • 19
    • 33845307613 scopus 로고    scopus 로고
    • Global pairwise sequence alignment through mixed-integer linear programming: A template-free approach
    • McAllister, S. R., R. Rajgaria, and C. A. Floudas. 2007. Global pairwise sequence alignment through mixed-integer linear programming: a template-free approach. Optimization Methods and Software. 22:127-144.
    • (2007) Optimization Methods and Software , vol.22 , pp. 127-144
    • McAllister, S.R.1    Rajgaria, R.2    Floudas, C.A.3
  • 21
    • 38649133822 scopus 로고    scopus 로고
    • A path selection approach to global pairwise sequence alignment using integer linear optimization
    • McAllister, S. R., R. Rajgaria, and C. A. Floudas. 2008. A path selection approach to global pairwise sequence alignment using integer linear optimization. Optimization. 57:101-111.
    • (2008) Optimization , vol.57 , pp. 101-111
    • McAllister, S.R.1    Rajgaria, R.2    Floudas, C.A.3
  • 23
    • 0027935740 scopus 로고
    • Multiple sequence alignment using simulated annealing
    • Kim, J., S. Pramanik, and M. J. Chung. 1994. Multiple sequence alignment using simulated annealing. Comput. Appl. Biosci. 10:419-426.
    • (1994) Comput. Appl. Biosci , vol.10 , pp. 419-426
    • Kim, J.1    Pramanik, S.2    Chung, M.J.3
  • 24
    • 28844459463 scopus 로고    scopus 로고
    • Simulated annealing algorithm for the multiple sequence alignment problem: The approach of polymers in a random medium
    • Hernández-Guía, M., R. Mulet, and S. Rodríguez- Pérez. 2005. Simulated annealing algorithm for the multiple sequence alignment problem: the approach of polymers in a random medium. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 72:031915.
    • (2005) Phys. Rev. E Stat. Nonlin. Soft Matter Phys , vol.72 , pp. 031915
    • Hernández-Guía, M.1    Mulet, R.2    Rodríguez- Pérez, S.3
  • 25
    • 0029872694 scopus 로고    scopus 로고
    • SAGA: Sequence alignment by genetic algorithm
    • Notredame, C., and D. G. Higgins. 1996. SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res. 24:1515-1524.
    • (1996) Nucleic Acids Res , vol.24 , pp. 1515-1524
    • Notredame, C.1    Higgins, D.G.2
  • 26
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    • Lee, J., H. A. Scheraga, and S. Rackovsky. 1997. New optimization method for conformational energy calculations on polypeptides: conformational space annealing. J. Comput. Chem. 18:1222-1232.
    • (1997) J. Comput. Chem , vol.18 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 27
    • 0032146482 scopus 로고    scopus 로고
    • Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing
    • Lee, J., H. A. Scheraga, and S. Rackovsky. 1998. Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers. 46:103-116.
    • (1998) Biopolymers , vol.46 , pp. 103-116
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 28
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S., C. D. Gelatt, and M. P. Vecchi. 1983. Optimization by simulated annealing. Science. 220:671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 30
    • 0002472452 scopus 로고
    • Genetic algorithms and the optimal allocations of trials
    • Holland, J. 1973. Genetic algorithms and the optimal allocations of trials. SIAM J. Comput. 2:88-105.
    • (1973) SIAM J. Comput , vol.2 , pp. 88-105
    • Holland, J.1
  • 32
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li, Z., and H. A. Scheraga. 1987. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA. 84:6611-6615.
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 34
    • 0033514939 scopus 로고    scopus 로고
    • Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
    • Lee, J., A. Liwo, and H. A. Scheraga. 1999. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc. Natl. Acad. Sci. USA. 96:2025-2030.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 2025-2030
    • Lee, J.1    Liwo, A.2    Scheraga, H.A.3
  • 35
    • 0038542253 scopus 로고    scopus 로고
    • Vortex patterns and infinite degeneracy in the uniformly frustrated XY models and lattice Coulomb gas
    • Ko, M. K., S. J. Lee, J. Lee, and B. Kim. 2003. Vortex patterns and infinite degeneracy in the uniformly frustrated XY models and lattice Coulomb gas. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 67:046120.
    • (2003) Phys. Rev. E Stat. Nonlin. Soft Matter Phys , vol.67 , pp. 046120
    • Ko, M.K.1    Lee, S.J.2    Lee, J.3    Kim, B.4
  • 36
    • 0141904480 scopus 로고    scopus 로고
    • Unbiased global optimization of Lennard-Jones clusters for N ≤ 201 using the conformational space annealing method
    • Lee, J., I. H. Lee, and J. Lee. 2003. Unbiased global optimization of Lennard-Jones clusters for N ≤ 201 using the conformational space annealing method. Phys. Rev. Lett. 91:080201.
    • (2003) Phys. Rev. Lett , vol.91 , pp. 080201
    • Lee, J.1    Lee, I.H.2    Lee, J.3
  • 37
    • 36148938374 scopus 로고    scopus 로고
    • Ground-state energy and energy landscape of the Sherrington-Kirkpatrick spin glass
    • Kim, S. Y., S. J. Lee, and J. Lee. 2007. Ground-state energy and energy landscape of the Sherrington-Kirkpatrick spin glass. Phys. Rev. B. 76:184412.
    • (2007) Phys. Rev. B , vol.76 , pp. 184412
    • Kim, S.Y.1    Lee, S.J.2    Lee, J.3
  • 39
    • 0032988850 scopus 로고    scopus 로고
    • BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
    • Thompson, J., F. Plewniak, and O. Poch. 1999. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics. 15:87-88.
    • (1999) Bioinformatics , vol.15 , pp. 87-88
    • Thompson, J.1    Plewniak, F.2    Poch, O.3
  • 40
    • 0031766401 scopus 로고    scopus 로고
    • HOMSTRAD: A database of protein structure alignments for homologous families
    • Mizuguchi, K., C. M. Deane, T. L. Blundell, and J. P. Overington. 1998. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 7:2469-2471.
    • (1998) Protein Sci , vol.7 , pp. 2469-2471
    • Mizuguchi, K.1    Deane, C.M.2    Blundell, T.L.3    Overington, J.P.4
  • 42
    • 36749030503 scopus 로고    scopus 로고
    • High accuracy template based modeling by global optimization
    • Joo, K., J. Lee, S. Lee, J.-H. Seo, S. J. Lee, and J. Lee. 2007. High accuracy template based modeling by global optimization. Proteins. 69(Suppl 8):83-89.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 83-89
    • Joo, K.1    Lee, J.2    Lee, S.3    Seo, J.-H.4    Lee, S.J.5    Lee, J.6
  • 43
    • 36749059956 scopus 로고    scopus 로고
    • Assessment of CASP7 predictions in the high accuracy template-based modeling category
    • Read, R. J., and G. Chavali. 2007. Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins. 69(Suppl 8):27-37.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 27-37
    • Read, R.J.1    Chavali, G.2


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