메뉴 건너뛰기




Volumn 11, Issue 5, 2012, Pages 175-182

Coordinated evolution of the Hepatitis B Virus Polymerase

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED DNA POLYMERASE; VIRUS PROTEIN;

EID: 84872447164     PISSN: 14343207     EISSN: None     Source Type: Journal    
DOI: 10.3233/ISB-2012-0452     Document Type: Article
Times cited : (9)

References (41)
  • 1
    • 3242881590 scopus 로고    scopus 로고
    • CRASP: A program for analysis of coordinated substitutions in multiple alignments of protein sequences
    • DOI 10.1093/nar/gkh451
    • Afonnikov, D. and N. Kolchanov, CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences. Nucleic Acids Res, 2004. 32: p.W64-W68. (Pubitemid 38997302)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Afonnikov, D.A.1    Kolchanov, N.A.2
  • 2
    • 0035182669 scopus 로고    scopus 로고
    • Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions
    • Afonnikov, D., D. Oshchepkov, and N. Kolchanov, Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. Bioinformatics, 2001. 17(11): p. 1035-1046. (Pubitemid 33085610)
    • (2001) Bioinformatics , vol.17 , Issue.11 , pp. 1035-1046
    • Afonnikov, D.A.1    Oshchepkov, D.Y.2    Kolchanov, N.A.3
  • 3
    • 0024974791 scopus 로고
    • Weights for data related by a tree
    • Altschul, S., R. Carroll, and D. Lipman, Weights for data related by a tree. J Mol Biol., 1989. 207(4): p. 647-653.
    • (1989) J Mol Biol. , vol.207 , Issue.4 , pp. 647-653
    • Altschul, S.1    Carroll, R.2    Lipman, D.3
  • 6
    • 61749095537 scopus 로고    scopus 로고
    • Genome-wide hepatitis C virus amino acid covariance networks can predict response to antiviral therapy in humans
    • Aurora, R., et al., Genome-wide hepatitis C virus amino acid covariance networks can predict response to antiviral therapy in humans. J Clin Invest, 2009. 119(1): p. 225-236.
    • (2009) J Clin Invest , vol.119 , Issue.1 , pp. 225-236
    • Aurora, R.1
  • 7
    • 2542529262 scopus 로고    scopus 로고
    • Pajek - Analysis and visualization of large networks
    • M. Juenger and P. Mutzel, Editors. Springer: Berlin.
    • Batagelj, V. and A. Mrvar, Pajek - Analysis and Visualization of Large Networks, in Graph Drawing Software, M. Juenger and P. Mutzel, Editors. 2003, Springer: Berlin. p. 77-103.
    • (2003) Graph Drawing Software , pp. 77-103
    • Batagelj, V.1    Mrvar, A.2
  • 8
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal statistical Society, Series B, 1995. 57(1): p. 289-300.
    • (1995) Journal of the Royal Statistical Society, Series B , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 9
    • 84986512474 scopus 로고
    • Charmm: A program for macromolecular energy, minimization, and dynamics calculations
    • Brooks, B., et al., CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J Comp Chem, 1983. 4: p. 187-217.
    • (1983) J Comp Chem , vol.4 , pp. 187-217
    • Brooks, B.1
  • 10
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motifs
    • DOI 10.1006/jmbi.1998.1943
    • Bystroff, C. and D. Baker, Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol, 1998. 281: p. 565-577. (Pubitemid 28372132)
    • (1998) Journal of Molecular Biology , vol.281 , Issue.3 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 11
    • 0043222570 scopus 로고    scopus 로고
    • Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA
    • Bystroff, C. and Y. Shao, Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA. Bioinformatics 2002. 18 (Suppl 1): p. S54-S61. (Pubitemid 41185637)
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Bystroff, C.1    Shao, Y.2
  • 14
    • 64549125990 scopus 로고    scopus 로고
    • Early changes of hepatitis B virus quasispecies during lamivudine treatment and the correlation with antiviral efficacy
    • Chen, L., et al., Early changes of hepatitis B virus quasispecies during lamivudine treatment and the correlation with antiviral efficacy. J Hepatol, 2009. 50(5): p. 895-905.
    • (2009) J Hepatol , vol.50 , Issue.5 , pp. 895-905
    • Chen, L.1
  • 16
    • 14844342815 scopus 로고    scopus 로고
    • The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
    • DOI 10.1016/j.jmb.2005.01.071
    • Dosztányi, Z., et al., The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins. J Mol Biol, 2005. 347: p. 827-839. (Pubitemid 40357923)
    • (2005) Journal of Molecular Biology , vol.347 , Issue.4 , pp. 827-839
    • Dosztanyi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 18
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar, R., MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 2004. 32(5): p. 1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 19
    • 0022203256 scopus 로고
    • Phylogenies and the comparative method
    • Felsenstein, J., Phylogenies and the comparative method. Am Nat, 1985. 125: p. 1-15.
    • (1985) Am Nat , vol.125 , pp. 1-15
    • Felsenstein, J.1
  • 21
    • 33646368672 scopus 로고    scopus 로고
    • Hepatitis B virus: Molecular virology and common mutants
    • DOI 10.1055/s-2006-939754
    • Harrison, T.J., Hepatitis B virus: molecular virology and common mutants. Semin Liver Dis, 2006. 26(2): p. 87-96. (Pubitemid 43668251)
    • (2006) Seminars in Liver Disease , vol.26 , Issue.2 , pp. 87-96
    • Harrison, T.J.1
  • 22
    • 0343621535 scopus 로고    scopus 로고
    • AAindex: Amino acid index database
    • Kawashima, S. and M. Kanehisa, AAindex: amino acid index database. Nucleic Acids Res, 2000. 28: p. 374. (Pubitemid 30047811)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 374
    • Kawashima, S.1    Kanehisa, M.2
  • 23
    • 77953465335 scopus 로고    scopus 로고
    • Coevolution and HBV drug resistance
    • Khudyakov, Y., Coevolution and HBV drug resistance. Antivir Ther, 2010. 15(3 Pt B): p. 505-515.
    • (2010) Antivir Ther , vol.15 , Issue.3 PART B , pp. 505-515
    • Khudyakov, Y.1
  • 24
    • 0024500958 scopus 로고
    • Prediction of terminal protein and ribonuclease H domains in the gene P product of hepadnaviruses
    • DOI 10.1016/0014-5793(89)80110-3
    • Khudyakov, Y. and A. Makhov, Prediction of terminal protein and ribonuclease H domains in the gene P product of hepadnaviruses. FEBS Lett, 1989. 243(2): p. 115-118. (Pubitemid 19037465)
    • (1989) FEBS Letters , vol.243 , Issue.2 , pp. 115-118
    • Khudyakov Yu., E.1    Makhov, A.M.2
  • 25
    • 17744395033 scopus 로고    scopus 로고
    • Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments
    • DOI 10.1093/bioinformatics/bti320
    • Kosakovsky, S. and S. Frost, Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics, 2005. 21(10): p. 2531-2533. (Pubitemid 40731616)
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2531-2533
    • Kosakovsky Pond, S.L.1    Frost, S.D.W.2
  • 26
    • 17744396121 scopus 로고    scopus 로고
    • Not so different after all: A comparison of methods for detecting amino acid sites under selection
    • DOI 10.1093/molbev/msi105
    • Kosakovsky, S. and S. Frost, Not so different after all: A comparison of methods for detecting amino acid sites under selection. Mol Biol Evol, 2005. 22(5): p. 1208-1222. (Pubitemid 40577758)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.5 , pp. 1208-1222
    • Kosakovsky Pond, S.L.1    Frost, S.D.W.2
  • 27
    • 15844406550 scopus 로고    scopus 로고
    • HyPhy: Hypothesis testing using phylogenies
    • DOI 10.1093/bioinformatics/bti079
    • Kosakovsky, S., S. Frost, and S. Muse, HyPhy: hypothesis testing using phylogenies. Bioinformatics, 2005. 21(5): p. 676-679. (Pubitemid 40424796)
    • (2005) Bioinformatics , vol.21 , Issue.5 , pp. 676-679
    • Kosakovsky Pond, S.L.1    Frost, S.D.W.2    Muse, S.V.3
  • 29
    • 84872468525 scopus 로고    scopus 로고
    • Mathworks,: Natick, MA. 7.11
    • Mathworks, Matlab version 7.11, 2010: Natick, MA.
    • (2010) Matlab Version
  • 30
    • 20844452182 scopus 로고    scopus 로고
    • Detection and reduction of evolutionary noise in correlated mutation analysis
    • DOI 10.1093/protein/gzi029
    • Noivirt, O., M. Eisenstein, and A. Horovitz, Detection and reduction of evolutionary noise in correlated mutation analysis. Protein Eng, 2005. 18(5): p. 247-253. (Pubitemid 40863429)
    • (2005) Protein Engineering, Design and Selection , vol.18 , Issue.5 , pp. 247-253
    • Noivirt, O.1    Eisenstein, M.2    Horovitz, A.3
  • 31
    • 54749091200 scopus 로고    scopus 로고
    • Supportive role played by precore and preS2 genomic changes in the establishment of lamivudine-resistant hepatitis B virus
    • Ohkawa, K., et al., Supportive role played by precore and preS2 genomic changes in the establishment of lamivudine-resistant hepatitis B virus. J Infect Dis, 2008. 198(8): p. 1150-1158.
    • (2008) J Infect Dis , vol.198 , Issue.8 , pp. 1150-1158
    • Ohkawa, K.1
  • 32
    • 50549084385 scopus 로고    scopus 로고
    • Spidermonkey: Rapid detection of co-evolving sites using Bayesian graphical models
    • Poon, A.F., et al., Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. Bioinformatics, 2008. 24(17): p. 1949-1950.
    • (2008) Bioinformatics , vol.24 , Issue.17 , pp. 1949-1950
    • Poon, A.F.1
  • 33
    • 36948998606 scopus 로고    scopus 로고
    • An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope
    • Poon, A.F., et al., An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol, 2007. 3(11): p. e231.
    • (2007) PLoS Comput Biol , vol.3 , Issue.11
    • Poon, A.F.1
  • 34
    • 0025061039 scopus 로고
    • Mutational analysis of the hepatitis B virus P gene product: Domain structure and RNase H activity
    • Radziwill, G., W. Tucker, and H. Schaller, Mutational analysis of the hepatitis B virus P gene product: domain structure and RNase H activity. J Virol, 1990. 64(2): p. 613-620. (Pubitemid 20032673)
    • (1990) Journal of Virology , vol.64 , Issue.2 , pp. 613-620
    • Radziwill, G.1    Tucker, W.2    Schaller, H.3
  • 35
    • 80052939676 scopus 로고    scopus 로고
    • Evaluation of intra-host Variants of the entire hepatitis B virus genome
    • doi: 10.1371/journal.pone.0025232
    • Ramachandran S., et al., Evaluation of intra-host Variants of the entire hepatitis B virus genome. PLoS ONE, 2011. 6(9): p. e25232. doi: 10.1371/journal.pone.0025232.
    • (2011) PLoS ONE , vol.6 , Issue.9
    • Ramachandran, S.1
  • 37
    • 80052897318 scopus 로고    scopus 로고
    • Genotypic distribution of hepatitis b virus (hbv) among acute cases of hbv infection, selected united states counties, 1999-2005
    • Teshale, E.H., et al., Genotypic distribution of hepatitis B virus (HBV) among acute cases of HBV infection, selected United States counties, 1999-2005. Clin Infect Dis, 2011. 53(8): p. 751-756.
    • (2011) Clin Infect Dis , vol.53 , Issue.8 , pp. 751-756
    • Teshale, E.H.1
  • 39
    • 0025398721 scopus 로고
    • WHAT IF. A molecular modeling and drug design program
    • DOI 10.1016/0263-7855(90)80070-V
    • Vriend, G., WHAT IF: A molecular modeling and drug design program. J Mol Graph, 1990. 8: p. 52-56. (Pubitemid 20717037)
    • (1990) Journal of Molecular Graphics , vol.8 , Issue.1 , pp. 52-56
    • Vriend, G.1
  • 40
    • 0036134765 scopus 로고    scopus 로고
    • Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
    • Yang, Z. and W. Swanson, Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol Biol Evol, 2002. 19(1): p. 49-57. (Pubitemid 34008046)
    • (2002) Molecular Biology and Evolution , vol.19 , Issue.1 , pp. 49-57
    • Yang, Z.1    Swanson, W.J.2
  • 41
    • 70350095437 scopus 로고    scopus 로고
    • Hepatitis B virus resistance to nucleos(t)ide analogues
    • e1-2
    • Zoulim, F. and S. Locarnini, Hepatitis B virus resistance to nucleos(t)ide analogues. Gastroenterology, 2009. 137(5): p. 1593-1608 e1-2.
    • (2009) Gastroenterology , vol.137 , Issue.5 , pp. 1593-1608
    • Zoulim, F.1    Locarnini, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.