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Volumn 28, Issue 3, 2012, Pages 331-341

Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; PROTEIN;

EID: 84856577919     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr657     Document Type: Article
Times cited : (107)

References (31)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 2
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 3
    • 77954257799 scopus 로고    scopus 로고
    • ConSurf 2010, calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    • Ashkenazy, H. et al. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res., 38, W529-W533.
    • (2010) Nucleic Acids Res , vol.38
    • Ashkenazy, H.1
  • 4
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • Capra, J.A. and Singh, M. (2007) Predicting functionally important residues from sequence conservation. Bioinformatics, 23, 1875-1882.
    • (2007) Bioinformatics , vol.23 , pp. 1875-1882
    • Capra, J.A.1    Singh, M.2
  • 5
    • 77950471248 scopus 로고    scopus 로고
    • Identification of ATP binding residues of a protein from its primary sequence
    • Chauhan, J.S. et al. (2009) Identification of ATP binding residues of a protein from its primary sequence. BMC Bioinformatics, 10, 434.
    • (2009) BMC Bioinformatics , vol.10 , pp. 434
    • Chauhan, J.S.1
  • 6
    • 77952971734 scopus 로고    scopus 로고
    • Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information
    • Chauhan, J.S., et al. (2010) Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information. BMC Bioinformatics, 11, 301.
    • (2010) BMC Bioinformatics , vol.11 , pp. 301
    • Chauhan, J.S.1
  • 7
    • 34249699005 scopus 로고    scopus 로고
    • Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs
    • Chen, K., et al. (2007) Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs. BMC Struct Biol., 7, 25.
    • (2007) BMC Struct Biol , vol.7 , pp. 25
    • Chen, K.1
  • 8
    • 58149269554 scopus 로고    scopus 로고
    • Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs
    • Chen, K., et al. (2009) Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs. J. Comput. Chem., 30, 163-172.
    • (2009) J. Comput. Chem. , vol.30 , pp. 163-172
    • Chen, K.1
  • 9
    • 84862006528 scopus 로고    scopus 로고
    • Investigation of atomic level patterns in protein-small ligand interactions
    • Chen, K. and Kurgan, L. (2009) Investigation of atomic level patterns in protein-small ligand interactions. PLoS ONE, 4, e4473.
    • (2009) PLoS ONE , vol.4
    • Chen, K.1    Kurgan, L.2
  • 10
    • 0034651543 scopus 로고    scopus 로고
    • When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families
    • Denessiouk, K.A. and Johnson, M.S. (2000) When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Proteins., 38, 310-326.
    • (2000) Proteins. , vol.38 , pp. 310-326
    • Denessiouk, K.A.1    Johnson, M.S.2
  • 11
    • 38549088882 scopus 로고    scopus 로고
    • LigASite-a database of biologically relevant binding sites in proteins with known apo-structures
    • Dessailly, B.H. et al. (2008) LigASite-a database of biologically relevant binding sites in proteins with known apo-structures. Nucleic Acids Res., 36, D667-D673.
    • (2008) Nucleic Acids Res. , vol.36
    • Dessailly, B.H.1
  • 12
    • 29144499905 scopus 로고    scopus 로고
    • Working set selection using second order information for training SVM
    • Fan, R.E. et al. (2005)Working set selection using second order information for training SVM. J. Mach. Learn Res., 6, 1889-1918.
    • (2005) J. Mach. Learn Res. , vol.6 , pp. 1889-1918
    • Fan, R.E.1
  • 13
    • 50949133669 scopus 로고    scopus 로고
    • LIBLINEAR: a library for large linear classification
    • Fan, R.E. et al. (2008) LIBLINEAR: a library for large linear classification. J. Mach. Learn. Res., 9, 1871-1874.
    • (2008) J. Mach. Learn. Res. , vol.9 , pp. 1871-1874
    • Fan, R.E.1
  • 14
    • 61449123967 scopus 로고    scopus 로고
    • Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network
    • Faraggi, E. et al. (2009) Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network. Proteins., 74, 847-856.
    • (2009) Proteins. , vol.74 , pp. 847-856
    • Faraggi, E.1
  • 15
    • 79955829108 scopus 로고    scopus 로고
    • Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates
    • Firoz, A. et al. (2011) Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates. BMC Biochem., 12, 20.
    • (2011) BMC Biochem. , vol.12 , pp. 20
    • Firoz, A.1
  • 16
    • 17244371152 scopus 로고
    • Correlation between a discrete and a continuous variable Point-biserial correlation
    • Tate, R.F. (1954) Correlation between a discrete and a continuous variable. Point-biserial correlation. Annals of Mathematical Statistics, 25, 603-607.
    • (1954) Annals of Mathematical Statistics , vol.25 , pp. 603-607
    • Tate, R.F.1
  • 17
    • 0036081122 scopus 로고    scopus 로고
    • LIGAND: database of chemical compounds and reactions in biological pathways
    • Goto, S. et al. (2002) LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res., 30, 402-404.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 402-404
    • Goto, S.1
  • 18
    • 36448991500 scopus 로고    scopus 로고
    • Clustal W and Clustal X version 2.0
    • Larkin, M.A. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Larkin, M.A.1
  • 19
    • 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
  • 20
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe, N.M. et al. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1
  • 21
    • 0842289654 scopus 로고    scopus 로고
    • Molecular determinants forATP-binding in proteins: a data mining and quantum chemical analysis
    • Mao, L., et al. (2004) Molecular determinants forATP-binding in proteins: a data mining and quantum chemical analysis. J. Mol. Biol., 336, 787-807.
    • (2004) J. Mol. Biol. , vol.336 , pp. 787-807
    • Mao, L.1
  • 22
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin, L.J. et al. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1
  • 23
    • 0030297640 scopus 로고    scopus 로고
    • Protein recognition of adenylate: an example of a fuzzy recognition template
    • Moodie, S.L. et al. (1996) Protein recognition of adenylate: an example of a fuzzy recognition template. J. Mol. Biol., 263, 486-500.
    • (1996) J. Mol. Biol. , vol.263 , pp. 486-500
    • Moodie, S.L.1
  • 24
    • 0035504287 scopus 로고    scopus 로고
    • On the molecular discrimination between adenine and guanine by proteins
    • Nobeli, I. et al. (2001) On the molecular discrimination between adenine and guanine by proteins. Nucleic Acids Res., 29, 4294-4309.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 4294-4309
    • Nobeli, I.1
  • 25
    • 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. et al. (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), S71-77.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Pupko, T.1
  • 26
    • 31544440473 scopus 로고    scopus 로고
    • An empirical approach for detecting nucleotide-binding sites on proteins
    • Saito, M. et al. (2006) An empirical approach for detecting nucleotide-binding sites on proteins. Protein Eng. Des. Sel., 19, 67-75.
    • (2006) Protein Eng. Des. Sel. , vol.19 , pp. 67-75
    • Saito, M.1
  • 27
    • 0025048136 scopus 로고
    • The P-loop -Acommon motif inATP-binding and GTP-binding proteins
    • Saraste, M. et al. (1990) The P-loop -Acommon motif inATP-binding and GTP-binding proteins. Trends Biochem Sci., 15, 430-434.
    • (1990) Trends Biochem Sci. , vol.15 , pp. 430-434
    • Saraste, M.1
  • 28
    • 0034711958 scopus 로고    scopus 로고
    • Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions
    • Senes, A. et al. (2000) Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J. Mol. Biol., 296, 921-936.
    • (2000) J. Mol. Biol. , vol.296 , pp. 921-936
    • Senes, A.1
  • 29
    • 0001607723 scopus 로고
    • Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide-binding fold
    • Walker, J.E. et al. (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide-binding fold. EMBO J., 1, 945-951.
    • (1982) EMBO J. , vol.1 , pp. 945-951
    • Walker, J.E.1
  • 30
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang, G. and Dunbrack, R.L. Jr. (2003) PISCES: a protein sequence culling server. Bioinformatics, 19, 1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 31
    • 33748505263 scopus 로고    scopus 로고
    • Incorporating background frequency improves entropy-based residue conservation measures
    • Wang, K. and Samudrala, R. (2006) Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics, 7, 385.
    • (2006) BMC Bioinformatics , vol.7 , pp. 385
    • Wang, K.1    Samudrala, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.