메뉴 건너뛰기




Volumn 38, Issue SUPPL. 2, 2010, Pages

ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CLIENT SERVER APPLICATION; COMPUTER INTERFACE; GENETIC CONSERVATION; INFORMATION PROCESSING; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; RELIABILITY; SEQUENCE HOMOLOGY; COMPUTER PROGRAM; CONFORMATION; INTERNET; MOLECULAR EVOLUTION; PROTEIN CONFORMATION; SEQUENCE ANALYSIS;

EID: 77954257799     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq399     Document Type: Article
Times cited : (1547)

References (40)
  • 1
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E. and Ben-Tal, N. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163-164.
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 2
    • 23144448512 scopus 로고    scopus 로고
    • ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
    • Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T. and Ben-Tal, N. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res., 33, W299-W302.
    • (2005) Nucleic Acids Res. , vol.33
    • Landau, M.1    Mayrose, I.2    Rosenberg, Y.3    Glaser, F.4    Martz, E.5    Pupko, T.6    Ben-Tal, N.7
  • 3
  • 4
    • 4143051195 scopus 로고    scopus 로고
    • Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior
    • Mayrose, I., Graur, D., Ben-Tal, N. and Pupko, T. (2004) Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol. Biol. Evol., 21, 1781-1791.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1781-1791
    • Mayrose, I.1    Graur, D.2    Ben-Tal, N.3    Pupko, T.4
  • 5
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko, T., Bell, R.E., Mayrose, I., Glaser, F. and Ben-Tal, N. (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics, 18(Suppl 1), S71-S77.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL 1
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 8
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 11
    • 33746124556 scopus 로고    scopus 로고
    • Biomolecules in the computer: Jmol to the rescue
    • Herráez, A. (2006) Biomolecules in the computer: Jmol to the rescue. Biochem. Mol. Biol. Educ., 34, 255-261.
    • (2006) Biochem. Mol. Biol. Educ. , vol.34 , pp. 255-261
    • Herráez, A.1
  • 14
    • 0025264766 scopus 로고
    • GAL4 transcription factor is not a "zinc finger" but forms a Zn(II)2Cys6 binuclear cluster
    • Pan, T. and Coleman, J.E. (1990) GAL4 transcription factor is not a "zinc finger" but forms a Zn(II)2Cys6 binuclear cluster. Proc. Natl Acad. Sci. USA, 87, 2077-2081.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 2077-2081
    • Pan, T.1    Coleman, J.E.2
  • 15
    • 0023274870 scopus 로고
    • Genetic evidence that zinc is an essential co-factor in the DNA binding domain of GAL4 protein
    • Johnston, M. (1987) Genetic evidence that zinc is an essential co-factor in the DNA binding domain of GAL4 protein. Nature, 328, 353-355.
    • (1987) Nature , vol.328 , pp. 353-355
    • Johnston, M.1
  • 16
    • 0026547747 scopus 로고
    • DNA recognition by GAL4: structure of a protein-DNA complex
    • Marmorstein, R., Carey, M., Ptashne, M. and Harrison, S.C. (1992) DNA recognition by GAL4: structure of a protein-DNA complex. Nature, 356, 408-414.
    • (1992) Nature , vol.356 , pp. 408-414
    • Marmorstein, R.1    Carey, M.2    Ptashne, M.3    Harrison, S.C.4
  • 18
    • 0026711010 scopus 로고
    • Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases
    • Tamura, K. (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol. Biol. Evol., 9, 678-687.
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 678-687
    • Tamura, K.1
  • 19
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., Kishino, H. and Yano, T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22, 160-174.
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 20
    • 0002671410 scopus 로고
    • Some probabilistic and statisical problems on the analysis of DNA sequences
    • Tavare, S. (1986) Some probabilistic and statisical problems on the analysis of DNA sequences. Lect. Math. Life Sci., 17, 57-86.
    • (1986) Lect. Math. Life Sci. , vol.17 , pp. 57-86
    • Tavare, S.1
  • 21
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le, S.Q. and Gascuel, O. (2008) An improved general amino acid replacement matrix. Mol. Biol. Evol., 25, 1307-1320.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 22
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.
    • (1992) Comput. Appl. Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 24
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan, S. and Goldman, N. (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol., 18, 691-699.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 25
    • 0029974748 scopus 로고    scopus 로고
    • Model of amino acid substitution in proteins encoded by mitochondrial DNA
    • Adachi, J. and Hasegawa, M. (1996) Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol., 42, 459-468.
    • (1996) J. Mol. Evol. , vol.42 , pp. 459-468
    • Adachi, J.1    Hasegawa, M.2
  • 26
    • 0033920569 scopus 로고    scopus 로고
    • Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
    • Adachi, J., Waddell, P.J., Martin, W. and Hasegawa, M. (2000) Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol., 50, 348-358.
    • (2000) J. Mol. Evol. , vol.50 , pp. 348-358
    • Adachi, J.1    Waddell, P.J.2    Martin, W.3    Hasegawa, M.4
  • 28
    • 57049150788 scopus 로고    scopus 로고
    • The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures
    • Goldenberg, O., Erez, E., Nimrod, G. and Ben-Tal, N. (2009) The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res., 37, D323-D327.
    • (2009) Nucleic Acids Res. , vol.37
    • Goldenberg, O.1    Erez, E.2    Nimrod, G.3    Ben-Tal, N.4
  • 29
    • 38549097071 scopus 로고    scopus 로고
    • The universal protein resource (UniProt)
    • The UniProt Consortium
    • The UniProt Consortium. (2008) The universal protein resource (UniProt). Nucleic Acids Res., 36, D190-D195.
    • (2008) Nucleic Acids Res. , vol.36
  • 30
    • 34347388470 scopus 로고    scopus 로고
    • UniRef: comprehensive and non-redundant UniProt reference clusters
    • Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R. and Wu, C.H. (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics, 23, 1282-1288.
    • (2007) Bioinformatics , vol.23 , pp. 1282-1288
    • Suzek, B.E.1    Huang, H.2    McGarvey, P.3    Mazumder, R.4    Wu, C.H.5
  • 31
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost, B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
    • (1999) Protein Eng. , vol.12 , pp. 85-94
    • Rost, B.1
  • 32
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • Katoh, K. and Toh, H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform., 9, 286-298.
    • (2008) Brief. Bioinform. , vol.9 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 34
    • 46249095233 scopus 로고    scopus 로고
    • Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
    • Loytynoja, A. and Goldman, N. (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320, 1632-1635.
    • (2008) Science , vol.320 , pp. 1632-1635
    • Loytynoja, A.1    Goldman, N.2
  • 35
    • 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
  • 36
    • 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
  • 37
    • 33750736013 scopus 로고    scopus 로고
    • The accuracy of several multiple sequence alignment programs for proteins
    • Nuin, P.A., Wang, Z. and Tillier, E.R. (2006) The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics, 7, 471.
    • (2006) BMC Bioinformatics , vol.7 , pp. 471
    • Nuin, P.A.1    Wang, Z.2    Tillier, E.R.3
  • 39
    • 57049094420 scopus 로고    scopus 로고
    • Detection of functionally important regions in "hypothetical proteins" of known structure
    • Nimrod, G., Schushan, M., Steinberg, D.M. and Ben-Tal, N. (2008) Detection of functionally important regions in "hypothetical proteins" of known structure. Structure, 16, 1755-1763.
    • (2008) Structure , vol.16 , pp. 1755-1763
    • Nimrod, G.1    Schushan, M.2    Steinberg, D.M.3    Ben-Tal, N.4
  • 40
    • 62649160355 scopus 로고    scopus 로고
    • Identification of DNA-binding proteins using structural, electrostatic and evolutionary features
    • Nimrod, G., Szilagyi, A., Leslie, C. and Ben-Tal, N. (2009) Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. J. Mol. Biol., 387, 1040-1053.
    • (2009) J. Mol. Biol. , vol.387 , pp. 1040-1053
    • Nimrod, G.1    Szilagyi, A.2    Leslie, C.3    Ben-Tal, N.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.