References - 2qgnA: Difference between revisions

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*Beiko, R. G., T. J. Harlow, et al. (2005). "Highways of gene sharing in prokaryotes." Proc Natl Acad Sci U S A 102(40): 14332-7.
*Altschul, S. F., W. Gish, et al. (1990). "Basic local alignment search tool." J Mol Biol 215(3): 403-10.
 
*DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA.
 
*Genome Net Database Resources. (2008). “Motif search.” http://motif.genome.jp/
 
*Golovko, A., G. Hjalm, et al. (2000). "Cloning of a human tRNA isopentenyl transferase." Gene 258(1-2): 85-93.
 
*Holm, L. and C. Sander (1997). "Dali/FSSP classification of three-dimensional protein folds." Nucleic Acids Res 25(1): 231-4.
 
*Hopper, A. K. and E. M. Phizicky (2003). "tRNA transfers to the limelight." Genes Dev 17(2): 162-80.


*Kohli, D. K. and A. K. Bachhawat (2003). "CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics." Nucleic Acids Res 31(13): 3501-2.
*Kohli, D. K. and A. K. Bachhawat (2003). "CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics." Nucleic Acids Res 31(13): 3501-2.


*NCBI. (2008). "National Center for Biotechnology Information." from http://www.ncbi.nlm.nih.gov/.
*Laskowski, R. A., N. M. Luscombe, et al. (1996). "Protein clefts in molecular recognition and function." Protein Sci 5(12): 2438-52.
 
*Laskowski, R. A., J. D. Watson, et al. (2005). "ProFunc: a server for predicting protein function from 3D structure." Nucleic Acids Res 33(Web Server issue): W89-93.


*Rambaut, A. (2006). "Institute of Evolutionary Biology, University of Edinburgh: FigTree Version 1.0." from http://tree.bio.ed.ac.uk/software/figtree/
*Liang, J., H. Edelsbrunner, et al. (1998). "Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design." Protein Sci 7(9): 1884-97.


*Holm L and Sander C. Dali/FSSP classification of three-dimensional protein folds Nucleic Acids Research. 25, 231-234 (1997)
*Martin N.A. and Hopper A.K. (1994). How single genes provide tRNA processing enzymes to mitochondria,nuclei and the cytosol. ''Biochimie'' 76 : 1161-1167


*Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB and Thornton JM. CATH - a hierarchic classification of protein domain structures. Structure. 5, 1093-1109 (1997)
*Martinsen, E. S., S. L. Perkins, et al. (2008). "A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): evolution of life-history traits and host switches." Mol Phylogenet Evol 47(1): 261-73.


*Laskowski RA, Watson JD and Thornton JM. ProFunc: a server for predicting protein function from 3D structure.Nucleic Acids Research. 33, W89-W93 (2005)
*NCBI. (2008). "National Center for Biotechnology Information." from http://www.ncbi.nlm.nih.gov/.


*DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA.
*Nesbo, C. L., Y. Boucher, et al. (2001). "Defining the core of nontransferable prokaryotic genes: the euryarchaeal core." J Mol Evol 53(4-5): 340-50.


*Function of protein. http://www.pantherdb.org/list/list.do?save=yes&searchModType=unfilterSpecies&filterLevel=1&listType=1&cutoff=1.0
*Orengo, C. A., A. D. Michie, et al. (1997). "CATH--a hierarchic classification of protein domain structures." Structure 5(8): 1093-108.


*Information about the gene encoding the protein, tRNA isopentenyltransferase 1 http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000005800
*Panther classification system. (2008). “Function of protein.” http://www.pantherdb.org/list/list.do?save=yes&searchModType=unfilterSpecies&filterLevel=1&listType=1&cutoff=1.0


*Sequence motifs of protein found using MotifFinder and Prosite. Retrieved from http://motif.genome.jp/motif-bin/Srch_Motif_Lib and http://ca.expasy.org/cgi-bin/prosite/ScanView.cgi?scanfile=79404153580.scan.gz
*Perez-Tris, J., D. Hasselquist, et al. (2005). "What are malaria parasites?" Trends Parasitol 21(5): 209-11.


*Function of tRNA-IPT. Retrieved from http://www.genesdev.org/cgi/reprint/17/2/162.pdf
*PROSITE (2008). “Database of protein domains, families and functional sites.” from http://ca.expasy.org/prosite/


'''Literature references'''
*Rambaut, A. (2006). "Institute of Evolutionary Biology, University of Edinburgh: FigTree Version 1.0." from http://tree.bio.ed.ac.uk/software/figtree/.


*Laskowski,R.A. , Luscombe,N.M. , Swindells,M.B. AND Thornton,M.J.(1994) Protein clefts in molecular recognition and function ''Protein Science'', 5:2438-2452.  
*Saraste, M., P. R. Sibbald, et al. (1990). "The P-loop--a common motif in ATP- and GTP-binding proteins." Trends Biochem Sci 15(11): 430-4.


*Martin N.A. and Hopper A.K. (1994). How single genes provide tRNA processing enzymes to mitochondria,nuclei and the cytosol. ''Biochimie'' 76 : 1161-1167
*Saccharomyces Genome Database.(2008). “Information about the gene encoding the protein, tRNA isopentenyltransferase 1.” http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000005800


*Golovko.A. , Hjalm.G , Sitbon.F. and Nicander.B.,.(2000). Cloning of a human tRNA isopentenyl transferase. ''Gene'' 258 (2000) 85–93.  
*Shi, J., T. L. Blundell, et al. (2001). "FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties." J Mol Biol 310(1): 243-57.


*The P-loop — a common motif in ATP- and GTP-binding proteins. Retrieved from http://www.sciencedirect.com.ezproxy.library.uq.edu.au/science?_ob=MImg&_imagekey=B6TCV-4864C9B-3K1&_cdi=5180&_user=331728&_orig=browse&_coverDate=11%2F30%2F1990&_sk=999849988&view=c&wchp=dGLbVtz-zSkzV&md5=aa860b3e9ffdbc0359bbf2d3be369038&ie=/sdarticle.pdf
*Voyich, J. M., D. E. Sturdevant, et al. (2008). "Analysis of Staphylococcus aureus gene expression during PMN phagocytosis." Methods Mol Biol 431: 109-22.


*Liang et al., (1998). Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. ''Protein Science'' : 71884-1897.
*Xie et al., (2007). Structure of tRNA dimethylallyltransferase: RNA modification through a channel. ''J. Mol. Biol.'' 367, 872–881


[[tRNA isopentenyl transferase 1|back to 2qgn]]
*Zharkikh, A. and W. H. Li (1992). "Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock." Mol Biol Evol 9(6): 1119-47.

Latest revision as of 06:11, 10 June 2008

  • Altschul, S. F., W. Gish, et al. (1990). "Basic local alignment search tool." J Mol Biol 215(3): 403-10.
  • DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA.
  • Golovko, A., G. Hjalm, et al. (2000). "Cloning of a human tRNA isopentenyl transferase." Gene 258(1-2): 85-93.
  • Holm, L. and C. Sander (1997). "Dali/FSSP classification of three-dimensional protein folds." Nucleic Acids Res 25(1): 231-4.
  • Hopper, A. K. and E. M. Phizicky (2003). "tRNA transfers to the limelight." Genes Dev 17(2): 162-80.
  • Kohli, D. K. and A. K. Bachhawat (2003). "CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics." Nucleic Acids Res 31(13): 3501-2.
  • Laskowski, R. A., N. M. Luscombe, et al. (1996). "Protein clefts in molecular recognition and function." Protein Sci 5(12): 2438-52.
  • Laskowski, R. A., J. D. Watson, et al. (2005). "ProFunc: a server for predicting protein function from 3D structure." Nucleic Acids Res 33(Web Server issue): W89-93.
  • Liang, J., H. Edelsbrunner, et al. (1998). "Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design." Protein Sci 7(9): 1884-97.
  • Martin N.A. and Hopper A.K. (1994). How single genes provide tRNA processing enzymes to mitochondria,nuclei and the cytosol. Biochimie 76 : 1161-1167
  • Martinsen, E. S., S. L. Perkins, et al. (2008). "A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): evolution of life-history traits and host switches." Mol Phylogenet Evol 47(1): 261-73.
  • Nesbo, C. L., Y. Boucher, et al. (2001). "Defining the core of nontransferable prokaryotic genes: the euryarchaeal core." J Mol Evol 53(4-5): 340-50.
  • Orengo, C. A., A. D. Michie, et al. (1997). "CATH--a hierarchic classification of protein domain structures." Structure 5(8): 1093-108.
  • Perez-Tris, J., D. Hasselquist, et al. (2005). "What are malaria parasites?" Trends Parasitol 21(5): 209-11.
  • Saraste, M., P. R. Sibbald, et al. (1990). "The P-loop--a common motif in ATP- and GTP-binding proteins." Trends Biochem Sci 15(11): 430-4.
  • Shi, J., T. L. Blundell, et al. (2001). "FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties." J Mol Biol 310(1): 243-57.
  • Voyich, J. M., D. E. Sturdevant, et al. (2008). "Analysis of Staphylococcus aureus gene expression during PMN phagocytosis." Methods Mol Biol 431: 109-22.
  • Xie et al., (2007). Structure of tRNA dimethylallyltransferase: RNA modification through a channel. J. Mol. Biol. 367, 872–881
  • Zharkikh, A. and W. H. Li (1992). "Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock." Mol Biol Evol 9(6): 1119-47.
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