메뉴 건너뛰기




Volumn 19, Issue 7, 2012, Pages 879-886

Optimization of profile-to-profile alignment parameters for one-dimensional threading

Author keywords

algorithms

Indexed keywords

PROTEIN;

EID: 84863915771     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0307     Document Type: Article
Times cited : (4)

References (35)
  • 1
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul, S.F., Gish, W., Miller, W., et al. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3
  • 3
    • 79956218804 scopus 로고    scopus 로고
    • Protein alignment algorithms with an efficient backtracking routine on multiple GPUs
    • Blazewicz, J., Frohmberg, W., Kierzynka, M., et al. 2011. Protein alignment algorithms with an efficient backtracking routine on multiple GPUs. BMC Bioinform. 12, 181.
    • (2011) BMC Bioinform. , vol.12 , pp. 181
    • Blazewicz, J.1    Frohmberg, W.2    Kierzynka, M.3
  • 7
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett, T. 2006. An introduction to ROC analysis. Patt. Recog. Lett. 27, 861-874.
    • (2006) Patt. Recog. Lett. , vol.27 , pp. 861-874
    • Fawcett, T.1
  • 9
    • 33644872068 scopus 로고    scopus 로고
    • BioShell - A package of tools for structural biology computations
    • DOI 10.1093/bioinformatics/btk037
    • Gront, D., and Kolinski, A. 2006. BioShell-a package of tools for structural biology computations. Bioinformatics 22, 621-622. (Pubitemid 43372826)
    • (2006) Bioinformatics , vol.22 , Issue.5 , pp. 621-622
    • Gront, D.1    Kolinski, A.2
  • 10
    • 39149134951 scopus 로고    scopus 로고
    • Utility library for structural bioinformatics
    • DOI 10.1093/bioinformatics/btm627
    • Gront, D., and Kolinski, A. 2008. Utility library for structural bioinformatics. Bioinformatics 24, 584-585. (Pubitemid 351256306)
    • (2008) Bioinformatics , vol.24 , Issue.4 , pp. 584-585
    • Gront, D.1    Kolinski, A.2
  • 11
    • 80052020052 scopus 로고    scopus 로고
    • Generalized fragment picking in rosetta: Design, protocols and applications
    • Gront, D., Kulp, D.W., Vernon, R.M., et al. 2011. Generalized fragment picking in rosetta: design, protocols and applications. PloS ONE 6, e23294+.
    • (2011) PloS ONE , vol.6
    • Gront, D.1    Kulp, D.W.2    Vernon, R.M.3
  • 12
    • 0035070578 scopus 로고    scopus 로고
    • Picasso: Generating a covering set of protein family profiles
    • Heger, A., and Holm, L. 2001. Picasso: generating a covering set of protein family profiles. Bioinformatics 17, 272-279. (Pubitemid 32288216)
    • (2001) Bioinformatics , vol.17 , Issue.3 , pp. 272-279
    • Heger, A.1    Holm, L.2
  • 13
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S., and Henikoff, J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915-10919.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 14
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • DOI 10.1006/jmbi.1999.3091
    • Jones, D.T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202. (Pubitemid 29435759)
    • (1999) Journal of Molecular Biology , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 15
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and Sander, C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 16
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • DOI 10.1093/bioinformatics/14.10.846
    • Karplus, K., Barrett, C., and Hughey, R. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics 14, 846-856. (Pubitemid 29041540)
    • (1998) Bioinformatics , vol.14 , Issue.10 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 17
    • 3242779291 scopus 로고    scopus 로고
    • Protein modeling and structure prediction with a reduced representation
    • Kolinski, A. 2004. Protein modeling and structure prediction with a reduced representation. Acta Biochim. Pol. 51, 349-371. (Pubitemid 38969298)
    • (2004) Acta Biochimica Polonica , vol.51 , Issue.2 , pp. 349-371
    • Kolinski, A.1
  • 18
    • 35748970173 scopus 로고    scopus 로고
    • Comparative modeling without implicit sequence alignments
    • DOI 10.1093/bioinformatics/btm380
    • Kolinski, A., and Gront, D. 2007. Comparative modeling without implicit sequence alignments. Bioinformatics 23, 2522-2527. (Pubitemid 350048353)
    • (2007) Bioinformatics , vol.23 , Issue.19 , pp. 2522-2527
    • Kolinski, A.1    Gront, D.2
  • 19
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • Lipman, D.J., and Pearson, W.R. 1985. Rapid and sensitive protein similarity searches. Science 227, 1435-1441. (Pubitemid 15146986)
    • (1985) Science , vol.227 , Issue.4693 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 20
    • 0041886960 scopus 로고    scopus 로고
    • Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments
    • DOI 10.1093/bioinformatics/btg185
    • Mittelman, D., Sadreyev, R., and Grishin, N. 2003. Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics 19, 1531-1539. (Pubitemid 37038869)
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1531-1539
    • Mittelman, D.1    Sadreyev, R.2    Grishin, N.3
  • 21
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T., et al. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3
  • 22
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S.B., and Wunsch, C.D. 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
  • 23
    • 33746091677 scopus 로고    scopus 로고
    • ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis
    • DOI 10.1109/TPDS.2006.112
    • Oehmen, C., and Nieplocha, J. 2006. ScalaBLAST: A Scalable Implementation of BLAST for high-performance dataintensive bioinformatics analysis. IEEE Trans. Parallel Distrib. Syst. 17, 740-749. (Pubitemid 44070144)
    • (2006) IEEE Transactions on Parallel and Distributed Systems , vol.17 , Issue.8 , pp. 740-749
    • Oehmen, C.1    Nieplocha, J.2
  • 24
    • 4444298729 scopus 로고    scopus 로고
    • Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods
    • DOI 10.1002/prot.20184
    • Ohlson, T., Wallner, B., and Elofsson, A. 2004. Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins 57, 188-197. (Pubitemid 39195892)
    • (2004) Proteins: Structure, Function and Genetics , vol.57 , Issue.1 , pp. 188-197
    • Ohlson, T.1    Wallner, B.2    Elofsson, A.3
  • 25
    • 0043130635 scopus 로고    scopus 로고
    • Profile-profile alignment: A powerful tool for protein structure prediction
    • von Ohsen, N., Sommer, I., and Zimmer, R. 2003. Profile-profile alignment: a powerful tool for protein structure prediction. Pac. Symp. Biocomput. 252-263.
    • (2003) Pac. Symp. Biocomput. , pp. 252-263
    • Von Ohsen, N.1    Sommer, I.2    Zimmer, R.3
  • 26
    • 0034628922 scopus 로고    scopus 로고
    • Combination of threading potentials and sequence profiles improves fold recognition
    • Panchenko, A.R., Marchler-Bauer, A., and Bryant, S.H. 2000. Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol. 296, 1319-1331.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1319-1331
    • Panchenko, A.R.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 27
    • 0037440190 scopus 로고    scopus 로고
    • Finding weak similarities between proteins by sequence profile comparison
    • DOI 10.1093/nar/gkg154
    • Panchenko, A.R. 2003. Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res. 31, 683-689. (Pubitemid 36175958)
    • (2003) Nucleic Acids Research , vol.31 , Issue.2 , pp. 683-689
    • Panchenko, A.R.1
  • 28
    • 0029789461 scopus 로고    scopus 로고
    • Searching databases of conserved sequence regions by aligning protein multiple-alignments
    • DOI 10.1093/nar/24.19.3836
    • Pietrokovski, S. 1996. Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res. 24, 3836-3845. (Pubitemid 26335396)
    • (1996) Nucleic Acids Research , vol.24 , Issue.19 , pp. 3836-3845
    • Pietrokovski, S.1
  • 29
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski, L., Jaroszewski, L., Li, W., et al. 2000. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 9, 232-241. (Pubitemid 30126996)
    • (2000) Protein Science , vol.9 , Issue.2 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 30
    • 0037423702 scopus 로고    scopus 로고
    • COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
    • DOI 10.1016/S0022-2836(02)01371-2
    • Sadreyev, R., and Grishin, N. 2003. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol. 326, 317-336. (Pubitemid 36279378)
    • (2003) Journal of Molecular Biology , vol.326 , Issue.1 , pp. 317-336
    • Sadreyev, R.1    Grishin, N.2
  • 31
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T.F., and Waterman, M.S. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 33
    • 2442663920 scopus 로고    scopus 로고
    • Scoring profile-to-profile sequence alignments
    • DOI 10.1110/ps.03601504
    • Wang, G., and Dunbrack, R.L. 2004. Scoring profile-to-profile sequence alignments. Prot. Sci. 13, 1612-1626. (Pubitemid 38669249)
    • (2004) Protein Science , vol.13 , Issue.6 , pp. 1612-1626
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 34
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
    • DOI 10.1006/jmbi.2001.5293
    • Yona, G., and Levitt, M. 2002. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J. Mol. Biol. 315, 1257-1275. (Pubitemid 34729302)
    • (2002) Journal of Molecular Biology , vol.315 , Issue.5 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 35
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • DOI 10.1093/nar/gki524
    • Zhang, Y., and Skolnick, J. 2005. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 33, 2302-2309. (Pubitemid 41439897)
    • (2005) Nucleic Acids Research , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.