메뉴 건너뛰기




Volumn 19, Issue 4, 2003, Pages 506-512

Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures

Author keywords

[No Author keywords available]

Indexed keywords

HYDROLASE; LIPOCALIN; NUCLEOTIDE;

EID: 0037339236     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg016     Document Type: Article
Times cited : (18)

References (24)
  • 2
    • 0035175770 scopus 로고    scopus 로고
    • BAl-iBASE (Benchmark Alignment dataBASE): Enhancements for repeats, transmembrane sequences and circular permutations
    • Bahr,A., Thompson,J.D., Thierry,J.C. and Poch,O. (2001) BAl-iBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res., 29, 323-326.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 323-326
    • Bahr, A.1    Thompson, J.D.2    Thierry, J.C.3    Poch, O.4
  • 4
    • 0036172167 scopus 로고    scopus 로고
    • Geno3D: Automatic comparative molecular modelling of protein
    • Combet,C., Jambon,M., DeleÌage,G. and Geourjon,C. (2002) Geno3D: automatic comparative molecular modelling of protein. Bioinformatics, 18, 213-214.
    • (2002) Bioinformatics , vol.18 , pp. 213-214
    • Combet, C.1    Jambon, M.2    DeleÌage, G.3    Geourjon, C.4
  • 5
    • 0034489478 scopus 로고    scopus 로고
    • Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments
    • Friedberg,I., Kaplan,T. and Margalit,H. (2000) Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments. Protein Sci., 9, 2278-2284.
    • (2000) Protein Sci. , vol.9 , pp. 2278-2284
    • Friedberg, I.1    Kaplan, T.2    Margalit, H.3
  • 6
    • 0029595442 scopus 로고
    • SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments
    • Geourjon,C. and DeleÌage,G. (1995) SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput. Appl. Biosci., 11, 681-684.
    • (1995) Comput. Appl. Biosci. , vol.11 , pp. 681-684
    • Geourjon, C.1    DeleÌage, G.2
  • 7
    • 0035082495 scopus 로고    scopus 로고
    • Identification of related proteins with weak sequence identity using secondary structure information
    • Geourjon,C., Combet,C., Blanchet,C. and DeleÌage,G. (2001) Identification of related proteins with weak sequence identity using secondary structure information. Protein Sci., 10, 788-797.
    • (2001) Protein Sci. , vol.10 , pp. 788-797
    • Geourjon, C.1    Combet, C.2    Blanchet, C.3    DeleÌage, G.4
  • 8
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 9
    • 0024974873 scopus 로고
    • Protozoan myoglobin from Paramecium caudatum its unusual amino acid sequence
    • Iwaasa,H., Takagi,T. and Shikama,K. (1989) Protozoan myoglobin from Paramecium caudatum its unusual amino acid sequence. J. Mol. Biol., 208, 355-358.
    • (1989) J. Mol. Biol. , vol.208 , pp. 355-358
    • Iwaasa, H.1    Takagi, T.2    Shikama, K.3
  • 10
    • 0032605879 scopus 로고    scopus 로고
    • Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure
    • Jones,D.T., Tress,M., Bryson,K. and Hadley,C. (1999) Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins, 37, 104-111.
    • (1999) Proteins , vol.37 , pp. 104-111
    • Jones, D.T.1    Tress, M.2    Bryson, K.3    Hadley, C.4
  • 11
    • 0034855972 scopus 로고    scopus 로고
    • Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set
    • Karplus,K. and Hu,B. (2001) Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics, 17, 713-720.
    • (2001) Bioinformatics , vol.17 , pp. 713-720
    • Karplus, K.1    Hu, B.2
  • 12
    • 0030827806 scopus 로고    scopus 로고
    • DSC: Public domain protein secondary structure predication
    • King,R.D., Saqi,M., Sayle,R. and Sternberg,M.J. (1997) DSC: public domain protein secondary structure predication. Comput. Appl. Biosci., 13, 473-474.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 473-474
    • King, R.D.1    Saqi, M.2    Sayle, R.3    Sternberg, M.J.4
  • 13
    • 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. and Chothia,C. (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    Chothia, C.4
  • 14
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: Calculation of positional conservation in a protein sequence alignment
    • Pei,J. and Grishin,N.V. (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17, 700-712.
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2
  • 15
    • 84983706152 scopus 로고    scopus 로고
    • Proteins 37; suppl. 3, 1999.
    • (1999) Proteins , vol.37
  • 16
    • 0028158628 scopus 로고
    • PHD: An automatic mail server for protein secondary structure prediction
    • Rost,B., Sander,C. and Schneider,R. (1994a) PHD: an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci., 10, 53-60.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 53-60
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 17
    • 0028064006 scopus 로고
    • Redefining the goals of protein secondary structure prediction
    • Rost,B., Sander,C. and Schneider,R. (1994b) Redefining the goals of protein secondary structure prediction. J. Mol. Biol., 235, 13-26.
    • (1994) J. Mol. Biol. , vol.235 , pp. 13-26
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 18
    • 0029186289 scopus 로고
    • TOPITS: Threading one-dimensional predictions into three-dimensional structures
    • Rost,B. (1995) TOPITS: threading one-dimensional predictions into three-dimensional structures. Proc. Int. Conf. Intell. Syst. Mol. Biol., 3, 314-321.
    • (1995) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.3 , pp. 314-321
    • Rost, B.1
  • 19
    • 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
  • 20
    • 0034062874 scopus 로고    scopus 로고
    • Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL
    • Teichmann,S.A., Chothia,C., Church,G.M. and Park,J. (2000) Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics, 16, 117-124.
    • (2000) Bioinformatics , vol.16 , pp. 117-124
    • Teichmann, S.A.1    Chothia, C.2    Church, G.M.3    Park, J.4
  • 21
    • 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., Higgins,D.G. and Gibson,T.J. (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
  • 22
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 23
    • 0035824873 scopus 로고    scopus 로고
    • Towards a reliable objective function for multiple sequence alignments
    • Thompson,J.D., Plewniak,F., Ripp,R., Thierry,J.C. and Poch,O. (2001) Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol., 314, 937-951.
    • (2001) J. Mol. Biol. , vol.314 , pp. 937-951
    • Thompson, J.D.1    Plewniak, F.2    Ripp, R.3    Thierry, J.C.4    Poch, O.5
  • 24
    • 0033081846 scopus 로고    scopus 로고
    • A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment
    • Zemla,A., Venclovas,C., Fidelis,K. and Rost,B. (1999) A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment. Proteins, 34, 220-223.
    • (1999) Proteins , vol.34 , pp. 220-223
    • Zemla, A.1    Venclovas, C.2    Fidelis, K.3    Rost, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.