-
1
-
-
38849083985
-
Hepatitis A virus mutant spectra under the selective pressure of monoclonal antibodies: codon usage constraints limit capsid variability
-
Aragones L., Bosch A., Pinto R.M. Hepatitis A virus mutant spectra under the selective pressure of monoclonal antibodies: codon usage constraints limit capsid variability. J. Virol. 2008, 82(4):1688-1700.
-
(2008)
J. Virol.
, vol.82
, Issue.4
, pp. 1688-1700
-
-
Aragones, L.1
Bosch, A.2
Pinto, R.M.3
-
2
-
-
77950421701
-
Fine-tuning translation kinetics selection as the driving force of codon usage bias in the hepatitis A virus capsid
-
Aragones L., Guix S., Ribes E., Bosch A., Pinto R.M. Fine-tuning translation kinetics selection as the driving force of codon usage bias in the hepatitis A virus capsid. PLoS Pathog. 2010, 6(3):e1000797.
-
(2010)
PLoS Pathog.
, vol.6
, Issue.3
-
-
Aragones, L.1
Guix, S.2
Ribes, E.3
Bosch, A.4
Pinto, R.M.5
-
3
-
-
73149095830
-
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences
-
Bahir I., Fromer M., Prat Y., Linial M. Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences. Mol. Syst. Biol. 2009, 5:311.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 311
-
-
Bahir, I.1
Fromer, M.2
Prat, Y.3
Linial, M.4
-
4
-
-
0033988512
-
Foot-and-mouth disease virus 3C protease induces cleavage of translation initiation factors eIF4A and eIF4G within infected cells
-
Belsham G.J., McInerney G.M., Ross-Smith N. Foot-and-mouth disease virus 3C protease induces cleavage of translation initiation factors eIF4A and eIF4G within infected cells. J. Virol. 2000, 74(1):272-280.
-
(2000)
J. Virol.
, vol.74
, Issue.1
, pp. 272-280
-
-
Belsham, G.J.1
McInerney, G.M.2
Ross-Smith, N.3
-
5
-
-
0020024572
-
Codon selection in yeast
-
Bennetzen J.L., Hall B.D. Codon selection in yeast. J. Biol. Chem. 1982, 257(6):3026-3031.
-
(1982)
J. Biol. Chem.
, vol.257
, Issue.6
, pp. 3026-3031
-
-
Bennetzen, J.L.1
Hall, B.D.2
-
6
-
-
15744372994
-
Crystal structure of foot-and-mouth disease virus 3C protease. New insights into catalytic mechanism and cleavage specificity
-
Birtley J.R., Knox S.R., Jaulent A.M., Brick P., Leatherbarrow R.J., Curry S. Crystal structure of foot-and-mouth disease virus 3C protease. New insights into catalytic mechanism and cleavage specificity. J. Biol. Chem. 2005, 280(12):11520-11527.
-
(2005)
J. Biol. Chem.
, vol.280
, Issue.12
, pp. 11520-11527
-
-
Birtley, J.R.1
Knox, S.R.2
Jaulent, A.M.3
Brick, P.4
Leatherbarrow, R.J.5
Curry, S.6
-
7
-
-
33746534916
-
Sequence analysis of the non-structural 3A and 3C protein-coding regions of foot-and-mouth disease virus serotype Asia1 field isolates from an endemic country
-
Biswas S., Sanyal A., Hemadri D., Tosh C., Mohapatra J.K., Manoj Kumar R., Bandyopadhyay S.K. Sequence analysis of the non-structural 3A and 3C protein-coding regions of foot-and-mouth disease virus serotype Asia1 field isolates from an endemic country. Vet. Microbiol. 2006, 116(1-3):187-193.
-
(2006)
Vet. Microbiol.
, vol.116
, Issue.1-3
, pp. 187-193
-
-
Biswas, S.1
Sanyal, A.2
Hemadri, D.3
Tosh, C.4
Mohapatra, J.K.5
Manoj Kumar, R.6
Bandyopadhyay, S.K.7
-
8
-
-
0029902243
-
Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level
-
Brunak S., Engelbrecht J. Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level. Proteins 1996, 25(2):237-252.
-
(1996)
Proteins
, vol.25
, Issue.2
, pp. 237-252
-
-
Brunak, S.1
Engelbrecht, J.2
-
9
-
-
18144374835
-
Comparative genomics of foot-and-mouth disease virus
-
Carrillo C., Tulman E.R., Delhon G., Lu Z., Carreno A., Vagnozzi A., Kutish G.F., Rock D.L. Comparative genomics of foot-and-mouth disease virus. J. Virol. 2005, 79(10):6487-6504.
-
(2005)
J. Virol.
, vol.79
, Issue.10
, pp. 6487-6504
-
-
Carrillo, C.1
Tulman, E.R.2
Delhon, G.3
Lu, Z.4
Carreno, A.5
Vagnozzi, A.6
Kutish, G.F.7
Rock, D.L.8
-
10
-
-
54849441249
-
Rare codons cluster
-
Clarke T.F.t., Clark P.L. Rare codons cluster. PLoS ONE 2008, 3(10):e3412.
-
(2008)
PLoS ONE
, vol.3
, Issue.10
-
-
Clarke, T.1
Clark, P.L.2
-
11
-
-
34250837503
-
Structural analysis of foot-and-mouth disease virus 3C protease: a viable target for antiviral drugs?
-
Curry S., Roque-Rosell N., Sweeney T.R., Zunszain P.A., Leatherbarrow R.J. Structural analysis of foot-and-mouth disease virus 3C protease: a viable target for antiviral drugs?. Biochem. Soc. Trans. 2007, 35(Pt 3):594-598.
-
(2007)
Biochem. Soc. Trans.
, vol.35
, Issue.PART 3
, pp. 594-598
-
-
Curry, S.1
Roque-Rosell, N.2
Sweeney, T.R.3
Zunszain, P.A.4
Leatherbarrow, R.J.5
-
12
-
-
33749649170
-
Foot-and-mouth disease virus 3C protease: recent structural and functional insights into an antiviral target
-
Curry S., Roque-Rosell N., Zunszain P.A., Leatherbarrow R.J. Foot-and-mouth disease virus 3C protease: recent structural and functional insights into an antiviral target. Int. J. Biochem. Cell Biol. 2007, 39(1):1-6.
-
(2007)
Int. J. Biochem. Cell Biol.
, vol.39
, Issue.1
, pp. 1-6
-
-
Curry, S.1
Roque-Rosell, N.2
Zunszain, P.A.3
Leatherbarrow, R.J.4
-
13
-
-
0344237338
-
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
-
dos Reis M., Wernisch L., Savva R. Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res. 2003, 31(23):6976-6985.
-
(2003)
Nucleic Acids Res.
, vol.31
, Issue.23
, pp. 6976-6985
-
-
dos Reis, M.1
Wernisch, L.2
Savva, R.3
-
15
-
-
0028802290
-
Identification of the active-site residues of the 3C proteinase of foot-and-mouth disease virus
-
Grubman M.J., Zellner M., Bablanian G., Mason P.W., Piccone M.E. Identification of the active-site residues of the 3C proteinase of foot-and-mouth disease virus. Virology 1995, 213(2):581-589.
-
(1995)
Virology
, vol.213
, Issue.2
, pp. 581-589
-
-
Grubman, M.J.1
Zellner, M.2
Bablanian, G.3
Mason, P.W.4
Piccone, M.E.5
-
16
-
-
0027218791
-
Folding of the MS2 coat protein in Escherichia coli is modulated by translational pauses resulting from mRNA secondary structure and codon usage: a hypothesis
-
Guisez Y., Robbens J., Remaut E., Fiers W. Folding of the MS2 coat protein in Escherichia coli is modulated by translational pauses resulting from mRNA secondary structure and codon usage: a hypothesis. J. Theor. Biol. 1993, 162(2):243-252.
-
(1993)
J. Theor. Biol.
, vol.162
, Issue.2
, pp. 243-252
-
-
Guisez, Y.1
Robbens, J.2
Remaut, E.3
Fiers, W.4
-
17
-
-
0034708361
-
Studies on the relationships between the synonymous codon usage and protein secondary structural units
-
Gupta S.K., Majumdar S., Bhattacharya T.K., Ghosh T.C. Studies on the relationships between the synonymous codon usage and protein secondary structural units. Biochem. Biophys. Res. Commun. 2000, 269(3):692-696.
-
(2000)
Biochem. Biophys. Res. Commun.
, vol.269
, Issue.3
, pp. 692-696
-
-
Gupta, S.K.1
Majumdar, S.2
Bhattacharya, T.K.3
Ghosh, T.C.4
-
18
-
-
0019949369
-
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs
-
Ikemura T. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J. Mol. Biol. 1982, 158(4):573-597.
-
(1982)
J. Mol. Biol.
, vol.158
, Issue.4
, pp. 573-597
-
-
Ikemura, T.1
-
19
-
-
0021958933
-
Codon usage and tRNA content in unicellular and multicellular organisms
-
Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 1985, 2(1):13-34.
-
(1985)
Mol. Biol. Evol.
, vol.2
, Issue.1
, pp. 13-34
-
-
Ikemura, T.1
-
20
-
-
58149199728
-
A pause for thought along the co-translational folding pathway
-
Komar A.A. A pause for thought along the co-translational folding pathway. Trends Biochem. Sci. 2009, 34(1):16-24.
-
(2009)
Trends Biochem. Sci.
, vol.34
, Issue.1
, pp. 16-24
-
-
Komar, A.A.1
-
21
-
-
66849109240
-
The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins
-
Kramer G., Boehringer D., Ban N., Bukau B. The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat. Struct. Mol. Biol. 2009, 16(6):589-597.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, Issue.6
, pp. 589-597
-
-
Kramer, G.1
Boehringer, D.2
Ban, N.3
Bukau, B.4
-
22
-
-
0030596612
-
The relation between codon usage, base correlation and gene expression level in Escherichia coli and yeast
-
Li H., Luo L. The relation between codon usage, base correlation and gene expression level in Escherichia coli and yeast. J. Theor. Biol. 1996, 181(2):111-124.
-
(1996)
J. Theor. Biol.
, vol.181
, Issue.2
, pp. 111-124
-
-
Li, H.1
Luo, L.2
-
23
-
-
0033539907
-
Compositional correlation studies among the three different codon positions in 12 bacterial genomes
-
Majumdar S., Gupta S.K., Sundararajan V.S., Ghosh T.C. Compositional correlation studies among the three different codon positions in 12 bacterial genomes. Biochem. Biophys. Res. Commun. 1999, 266(1):66-71.
-
(1999)
Biochem. Biophys. Res. Commun.
, vol.266
, Issue.1
, pp. 66-71
-
-
Majumdar, S.1
Gupta, S.K.2
Sundararajan, V.S.3
Ghosh, T.C.4
-
24
-
-
0036908375
-
Distribution of rare triplets along mRNA and their relation to protein folding
-
Makhoul C.H., Trifonov E.N. Distribution of rare triplets along mRNA and their relation to protein folding. J. Biomol. Struct. Dyn. 2002, 20(3):413-420.
-
(2002)
J. Biomol. Struct. Dyn.
, vol.20
, Issue.3
, pp. 413-420
-
-
Makhoul, C.H.1
Trifonov, E.N.2
-
25
-
-
0037232731
-
Molecular basis of pathogenesis of FMDV
-
Mason P.W., Grubman M.J., Baxt B. Molecular basis of pathogenesis of FMDV. Virus Res. 2003, 91(1):9-32.
-
(2003)
Virus Res.
, vol.91
, Issue.1
, pp. 9-32
-
-
Mason, P.W.1
Grubman, M.J.2
Baxt, B.3
-
26
-
-
0036017381
-
Translation initiation AUG context varies with codon usage bias and gene length in Drosophila melanogaster
-
Miyasaka H. Translation initiation AUG context varies with codon usage bias and gene length in Drosophila melanogaster. J. Mol. Evol. 2002, 55(1):52-64.
-
(2002)
J. Mol. Evol.
, vol.55
, Issue.1
, pp. 52-64
-
-
Miyasaka, H.1
-
27
-
-
0032493780
-
Specific correlations between relative synonymous codon usage and protein secondary structure
-
Oresic M., Shalloway D. Specific correlations between relative synonymous codon usage and protein secondary structure. J. Mol. Biol. 1998, 281(1):31-48.
-
(1998)
J. Mol. Biol.
, vol.281
, Issue.1
, pp. 31-48
-
-
Oresic, M.1
Shalloway, D.2
-
28
-
-
68249130936
-
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation
-
Parmley J.L., Huynen M.A. Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PLoS Genet. 2009, 5(7):e1000548.
-
(2009)
PLoS Genet.
, vol.5
, Issue.7
-
-
Parmley, J.L.1
Huynen, M.A.2
-
29
-
-
8744310123
-
Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization
-
Rocha E.P. Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res. 2004, 14(11):2279-2286.
-
(2004)
Genome Res.
, vol.14
, Issue.11
, pp. 2279-2286
-
-
Rocha, E.P.1
-
30
-
-
78049403925
-
Synonymous codon usage influences the local protein structure observed
-
Saunders R., Deane C.M. Synonymous codon usage influences the local protein structure observed. Nucleic Acids Res. 2010, 38(19):6719-6728.
-
(2010)
Nucleic Acids Res.
, vol.38
, Issue.19
, pp. 6719-6728
-
-
Saunders, R.1
Deane, C.M.2
-
31
-
-
0024405193
-
Codon usage determines translation rate in Escherichia coli
-
Sorensen M.A., Kurland C.G., Pedersen S. Codon usage determines translation rate in Escherichia coli. J. Mol. Biol. 1989, 207(2):365-377.
-
(1989)
J. Mol. Biol.
, vol.207
, Issue.2
, pp. 365-377
-
-
Sorensen, M.A.1
Kurland, C.G.2
Pedersen, S.3
-
32
-
-
0027968068
-
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., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22(22):4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
33
-
-
52949137359
-
Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima
-
Tsai C.J., Sauna Z.E., Kimchi-Sarfaty C., Ambudkar S.V., Gottesman M.M., Nussinov R. Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J. Mol. Biol. 2008, 383(2):281-291.
-
(2008)
J. Mol. Biol.
, vol.383
, Issue.2
, pp. 281-291
-
-
Tsai, C.J.1
Sauna, Z.E.2
Kimchi-Sarfaty, C.3
Ambudkar, S.V.4
Gottesman, M.M.5
Nussinov, R.6
-
34
-
-
67650687073
-
You're one in a googol: optimizing genes for protein expression
-
Welch M., Villalobos A., Gustafsson C., Minshull J. You're one in a googol: optimizing genes for protein expression. J. R. Soc. Interface 2009, 6(Suppl. 4):S467-S476.
-
(2009)
J. R. Soc. Interface
, vol.6
, Issue.SUPPL. 4
-
-
Welch, M.1
Villalobos, A.2
Gustafsson, C.3
Minshull, J.4
-
35
-
-
77956694182
-
Cell biology. New roles for codon usage
-
Weygand-Durasevic I., Ibba M. Cell biology. New roles for codon usage. Science 2010, 329(5998):1473-1474.
-
(2010)
Science
, vol.329
, Issue.5998
, pp. 1473-1474
-
-
Weygand-Durasevic, I.1
Ibba, M.2
-
36
-
-
0031697801
-
The relationship between synonymous codon usage and protein structure
-
Xie T., Ding D. The relationship between synonymous codon usage and protein structure. FEBS Lett. 1998, 434(1-2):93-96.
-
(1998)
FEBS Lett.
, vol.434
, Issue.1-2
, pp. 93-96
-
-
Xie, T.1
Ding, D.2
-
37
-
-
64549100262
-
Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis
-
Zhang G., Ignatova Z. Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis. PLoS ONE 2009, 4(4):e5036.
-
(2009)
PLoS ONE
, vol.4
, Issue.4
-
-
Zhang, G.1
Ignatova, Z.2
-
38
-
-
84872136109
-
The analysis of codon bias of foot-and-mouth disease virus and the adaptation of this virus to the hosts
-
Zhou J.H., Gao Z.L., Zhang J., Ding Y.Z., Stipkovits L., Szathmary S., Pejsak Z., Liu Y.S. The analysis of codon bias of foot-and-mouth disease virus and the adaptation of this virus to the hosts. Infect. Genet. Evol. 2013, 14C:105-110.
-
(2013)
Infect. Genet. Evol.
, vol.14 C
, pp. 105-110
-
-
Zhou, J.H.1
Gao, Z.L.2
Zhang, J.3
Ding, Y.Z.4
Stipkovits, L.5
Szathmary, S.6
Pejsak, Z.7
Liu, Y.S.8
-
39
-
-
67649356943
-
Translationally optimal codons associate with structurally sensitive sites in proteins
-
Zhou T., Weems M., Wilke C.O. Translationally optimal codons associate with structurally sensitive sites in proteins. Mol. Biol. Evol. 2009, 26(7):1571-1580.
-
(2009)
Mol. Biol. Evol.
, vol.26
, Issue.7
, pp. 1571-1580
-
-
Zhou, T.1
Weems, M.2
Wilke, C.O.3
|