메뉴 건너뛰기




Volumn 104, Issue 1-2, 2008, Pages 2-6

Protein homology modelling and its use in South Africa

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL DEVELOPMENT; COST-BENEFIT ANALYSIS; DISEASE; DRUG; HOMOLOGY; MODELING; PROTEIN;

EID: 44649097694     PISSN: 00382353     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review
Times cited : (16)

References (64)
  • 2
    • 73049141837 scopus 로고
    • The three-dimensional structure of a protein molecule
    • Kendrew J.C. (1961). The three-dimensional structure of a protein molecule. Sci. Am. 205(6), 96-110.
    • (1961) Sci. Am , vol.205 , Issue.6 , pp. 96-110
    • Kendrew, J.C.1
  • 3
    • 0033536636 scopus 로고    scopus 로고
    • Support for structural genomics and synchrotrons
    • Cassman M. and Norvell J.C. (1999). Support for structural genomics and synchrotrons. Science 286, 239-240.
    • (1999) Science , vol.286 , pp. 239-240
    • Cassman, M.1    Norvell, J.C.2
  • 6
    • 0033767942 scopus 로고    scopus 로고
    • Creating a structural genomics consortium
    • Williamson A.R. (2000). Creating a structural genomics consortium. Nature Struct. Biol. Suppl. 953.
    • (2000) Nature Struct. Biol , Issue.SUPPL. 953
    • Williamson, A.R.1
  • 7
    • 34347394165 scopus 로고    scopus 로고
    • Towards a comprehensive structural coverage of completed genomes: A structural genomics viewpoint
    • Marsden R.L., Lewis T.A. and Orengo C.A. (2007). Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC Bioinformatics 8, 86.
    • (2007) BMC Bioinformatics , vol.8 , pp. 86
    • Marsden, R.L.1    Lewis, T.A.2    Orengo, C.A.3
  • 8
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander C. and Schneider R. (1991). Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9, 56-68.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 9
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D. and Sali A. (2001). Protein structure prediction and structural genomics. Science 294, 93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 10
    • 3242813635 scopus 로고    scopus 로고
    • Utility of homology models in the drug discovery process
    • Hillisch A., Pineda L.F. and Hilgenfeld R. (2004). Utility of homology models in the drug discovery process. Drug Discov. Today 9, 659-669.
    • (2004) Drug Discov. Today , vol.9 , pp. 659-669
    • Hillisch, A.1    Pineda, L.F.2    Hilgenfeld, R.3
  • 15
    • 33744779891 scopus 로고    scopus 로고
    • Sequence comparison and protein structure prediction
    • Dunbrack R.L. Jr (2006). Sequence comparison and protein structure prediction. Curr. Opin. Struct. Biol. 16, 374-384.
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 374-384
    • Dunbrack Jr, R.L.1
  • 16
    • 33745076219 scopus 로고    scopus 로고
    • Advances in homology protein structure modeling
    • Xiang Z. (2006). Advances in homology protein structure modeling. Curr. Protein Pept. Sci. 7, 217-227.
    • (2006) Curr. Protein Pept. Sci , vol.7 , pp. 217-227
    • Xiang, Z.1
  • 18
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparison with FASTP and FASTA
    • Pearson W.R. (1990). Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183, 63-98.
    • (1990) Methods Enzymol , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 20
    • 0027122860 scopus 로고
    • Computer speed and sequence comparison
    • Barton G.J. (1992). Computer speed and sequence comparison. Science 257, 1609-1610.
    • (1992) Science , vol.257 , pp. 1609-1610
    • Barton, G.J.1
  • 21
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: A comprehensive database of protein domain families based on seed alignments
    • Sonhammer E.L., Eddy S.R. and Durbin R. (1997). Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28, 405-420.
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonhammer, E.L.1    Eddy, S.R.2    Durbin, R.3
  • 22
    • 0024234855 scopus 로고
    • CLUSTAL: A package for performing multiple sequence alignment on a microcomputer
    • Higgins D.G. and Sharp P.M. (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237-244.
    • (1988) Gene , vol.73 , pp. 237-244
    • Higgins, D.G.1    Sharp, P.M.2
  • 23
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar R.C. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 24
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for multiple sequence alignments
    • Notredame C., Higgins D. and Heringa J. (2000). T-Coffee: a novel method for multiple sequence alignments. J. Mol. Biol. 302, 205-217.
    • (2000) J. Mol. Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.2    Heringa, J.3
  • 25
    • 2942619012 scopus 로고    scopus 로고
    • 3DCoffee: Combining protein sequences and structures within multiple sequence alignments
    • O'Sullivan O., Suhre K., Abergel C., Higgins D.G. and Notredame C. (2004). 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 340, 385-395
    • (2004) J. Mol. Biol , vol.340 , pp. 385-395
    • O'Sullivan, O.1    Suhre, K.2    Abergel, C.3    Higgins, D.G.4    Notredame, C.5
  • 26
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi J., Blundell T.L. and Mizuguchi K. (2001). FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310, 243-257.
    • (2001) J. Mol. Biol , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 27
    • 0038634975 scopus 로고    scopus 로고
    • Improvement of the GenTHREADER method for genomic fold recognition
    • McGuffin L.J. and Jones D.T. (2003). Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19, 874-881.
    • (2003) Bioinformatics , vol.19 , pp. 874-881
    • McGuffin, L.J.1    Jones, D.T.2
  • 29
    • 0026754015 scopus 로고
    • Accurate modelling of protein conformation by automatic segment matching
    • Levitt M. (1992). Accurate modelling of protein conformation by automatic segment matching. J. Mol. Biol. 226, 507-533.
    • (1992) J. Mol. Biol , vol.226 , pp. 507-533
    • Levitt, M.1
  • 30
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A. and Blundell T.L. (1993). Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.
    • (1993) J. Mol. Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 32
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • Vriend G. (1990). WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8, 52-56.
    • (1990) J. Mol. Graph , vol.8 , pp. 52-56
    • Vriend, G.1
  • 33
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser A., Do R.K. and Sali A. (2000). Modeling of loops in protein structures. Protein Science 9, 1753-73.
    • (2000) Protein Science , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 35
    • 44649109517 scopus 로고    scopus 로고
    • Protein tertiary structure prediction
    • Cambridge University Press, Cambridge
    • Xiong J. (2006). Protein tertiary structure prediction. In Essential Bioinformatics, pp. 214-230. Cambridge University Press, Cambridge.
    • (2006) Essential Bioinformatics , pp. 214-230
    • Xiong, J.1
  • 37
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., Moss D.S. and Thornton J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
    • (1993) J. Appl. Cryst , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 40
    • 0032506030 scopus 로고    scopus 로고
    • Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
    • Sanchez R. and Sali A. (1998). Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl Acad. Sci. USA 95, 13597-13602.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 13597-13602
    • Sanchez, R.1    Sali, A.2
  • 41
    • 0032905858 scopus 로고    scopus 로고
    • A brighter future for protein structure prediction
    • Koehl P. and Levitt M. (1999). A brighter future for protein structure prediction. Nature Struct. Biol. 6, 108-111.
    • (1999) Nature Struct. Biol , vol.6 , pp. 108-111
    • Koehl, P.1    Levitt, M.2
  • 44
    • 13444291908 scopus 로고    scopus 로고
    • Homology modeling studies on human galactose-1-phosphate uridylytransferase and on its galactosemia-related mutant Q188R provide an explanation of molecular effects of the mutation on homo- and heterodimers
    • Marabotti A. and Facchiano A.M. (2005). Homology modeling studies on human galactose-1-phosphate uridylytransferase and on its galactosemia-related mutant Q188R provide an explanation of molecular effects of the mutation on homo- and heterodimers. J. Med. Chem. 48, 773-779.
    • (2005) J. Med. Chem , vol.48 , pp. 773-779
    • Marabotti, A.1    Facchiano, A.M.2
  • 45
    • 18044399158 scopus 로고    scopus 로고
    • A homology model for human α-L-iduronidase: Insights into human disease
    • Rempel B.P., Clarke L.A. and Withers S.G. (2005). A homology model for human α-L-iduronidase: insights into human disease. Mol. Genet. Metab. 85, 28-37.
    • (2005) Mol. Genet. Metab , vol.85 , pp. 28-37
    • Rempel, B.P.1    Clarke, L.A.2    Withers, S.G.3
  • 47
    • 0038120984 scopus 로고    scopus 로고
    • Coronavirus main proteinase (3CLpr) structure: Basis for design of anti-SARS drugs
    • Anand K., Ziebuhr J., Wadhwani P., Mesters J.R. and Hilgenfeld R. (2003). Coronavirus main proteinase (3CLpr) structure: basis for design of anti-SARS drugs. Science 300, 1763-1767.
    • (2003) Science , vol.300 , pp. 1763-1767
    • Anand, K.1    Ziebuhr, J.2    Wadhwani, P.3    Mesters, J.R.4    Hilgenfeld, R.5
  • 49
    • 0034658406 scopus 로고    scopus 로고
    • A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana
    • Suresh S., Turley S., Opperdoes F.R., Michels P.A. and Hol W.G. (2000). A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana. Structure 8, 541-552.
    • (2000) Structure , vol.8 , pp. 541-552
    • Suresh, S.1    Turley, S.2    Opperdoes, F.R.3    Michels, P.A.4    Hol, W.G.5
  • 50
    • 0036109555 scopus 로고    scopus 로고
    • Homology modeling and molecular dynamics study of NAD-dependent glycerol-3-phosphate dehydrogenase from Trypanosoma brucei rhodesiense, a potential target enzyme for anti-sleeping sickness drug development
    • Zubrzycki I.Z. (2002). Homology modeling and molecular dynamics study of NAD-dependent glycerol-3-phosphate dehydrogenase from Trypanosoma brucei rhodesiense, a potential target enzyme for anti-sleeping sickness drug development. Biophys. J. 82, 2906-2915.
    • (2002) Biophys. J , vol.82 , pp. 2906-2915
    • Zubrzycki, I.Z.1
  • 51
    • 0036015625 scopus 로고    scopus 로고
    • Amino acid sequence and structure modeling of savinin, a thrombin inhibitor from the tick, Ornithodoros savignyi
    • Mans B.J., Louw A.I and Neitz A.W.H. (2002). Amino acid sequence and structure modeling of savinin, a thrombin inhibitor from the tick, Ornithodoros savignyi. Insect Biochem. Mol. Biol. 32, 821-828.
    • (2002) Insect Biochem. Mol. Biol , vol.32 , pp. 821-828
    • Mans, B.J.1    Louw, A.I.2    Neitz, A.W.H.3
  • 52
    • 0034972445 scopus 로고    scopus 로고
    • The ears of the hippopotamus: Manifestations, determinants, and estimates of the malaria burden
    • Breman J. (2001). The ears of the hippopotamus: manifestations, determinants, and estimates of the malaria burden. Am. J. Trop. Med. Hyg. 64, 1-11.
    • (2001) Am. J. Trop. Med. Hyg , vol.64 , pp. 1-11
    • Breman, J.1
  • 53
    • 0037441470 scopus 로고    scopus 로고
    • Comparative properties of a three-dimensional model of Plasmodium falciparum ornithine decarboxylase
    • Birkholtz L., Joubert F., Neitz A.W.H. and Louw A.I. (2003). Comparative properties of a three-dimensional model of Plasmodium falciparum ornithine decarboxylase. Proteins 50, 464-473.
    • (2003) Proteins , vol.50 , pp. 464-473
    • Birkholtz, L.1    Joubert, F.2    Neitz, A.W.H.3    Louw, A.I.4
  • 54
    • 28944447254 scopus 로고    scopus 로고
    • Novel properties of malarial S-adenosylmethionine decarboxylase as revealed by structural modeling
    • Wells G.A., Birkholtz L.M., Joubert F., Walter R.D. and Louw A.I. (2006). Novel properties of malarial S-adenosylmethionine decarboxylase as revealed by structural modeling. J. Mol. Graph. Model. 24, 307-318.
    • (2006) J. Mol. Graph. Model , vol.24 , pp. 307-318
    • Wells, G.A.1    Birkholtz, L.M.2    Joubert, F.3    Walter, R.D.4    Louw, A.I.5
  • 55
    • 33847787279 scopus 로고    scopus 로고
    • Structural and mechanistic insights into the action of Plasmodium falciparum spermidine synthase
    • Burger P.B., Birkholtz L.M., Joubert F., Haider N., Walter R.D. and Louw A.I. (2007). Structural and mechanistic insights into the action of Plasmodium falciparum spermidine synthase. Bioorg. Med. Chem. 15, 1628-1637.
    • (2007) Bioorg. Med. Chem , vol.15 , pp. 1628-1637
    • Burger, P.B.1    Birkholtz, L.M.2    Joubert, F.3    Haider, N.4    Walter, R.D.5    Louw, A.I.6
  • 56
    • 33646542706 scopus 로고    scopus 로고
    • Elucidation of sulfadoxine resistance with structural models of the bifunctional Plasmodium falciparum dihydropterin pyrophosphokinase-dihydropteroate synthase
    • de Beer T.A.P., Louw A.I. and Joubert F. (2006). Elucidation of sulfadoxine resistance with structural models of the bifunctional Plasmodium falciparum dihydropterin pyrophosphokinase-dihydropteroate synthase. Bioorg. Med. Chem. 14, 4433-4443.
    • (2006) Bioorg. Med. Chem , vol.14 , pp. 4433-4443
    • de Beer, T.A.P.1    Louw, A.I.2    Joubert, F.3
  • 58
    • 29744451511 scopus 로고    scopus 로고
    • Oligomeric structure of nitrilases effect of mutating interfacial residues on activity
    • Sewell B.T., Thuku R.N., Zhang X. and Benedik M.J. (2005). Oligomeric structure of nitrilases effect of mutating interfacial residues on activity. Ann. N. Y. Acad. Sci. 1056, 153-159.
    • (2005) Ann. N. Y. Acad. Sci , vol.1056 , pp. 153-159
    • Sewell, B.T.1    Thuku, R.N.2    Zhang, X.3    Benedik, M.J.4
  • 59
    • 0242542014 scopus 로고    scopus 로고
    • The cyanide degrading nitrilase from Pseudomonas stutzeri AK61 is a two-fold symmetry, 14-subunit spiral
    • Sewell B.T., Berman M. and Meyers P.R. (2003). The cyanide degrading nitrilase from Pseudomonas stutzeri AK61 is a two-fold symmetry, 14-subunit spiral. Structure 11, 1413-1422.
    • (2003) Structure , vol.11 , pp. 1413-1422
    • Sewell, B.T.1    Berman, M.2    Meyers, P.R.3
  • 60
    • 0041528198 scopus 로고    scopus 로고
    • CynD, the cyanide dihydratase from Bacillus pumilus: Gene cloning, and structural studies
    • Jandhyala D., Berman M.N. and Meyers P.R. (2003). CynD, the cyanide dihydratase from Bacillus pumilus: gene cloning, and structural studies. Appl. Environ. Microbiol. 69, 4794-4805.
    • (2003) Appl. Environ. Microbiol , vol.69 , pp. 4794-4805
    • Jandhyala, D.1    Berman, M.N.2    Meyers, P.R.3
  • 61
    • 34247144173 scopus 로고    scopus 로고
    • Post-translational cleavage of recombinantly expressed nitrilase from Rhodococcus rhodochrous J1 yields a stable, active helical form
    • Thuku N.R., Weber B.W., Varsani A. and Sewell T. (2007). Post-translational cleavage of recombinantly expressed nitrilase from Rhodococcus rhodochrous J1 yields a stable, active helical form. FEBS J. 274, 2099-2108.
    • (2007) FEBS J , vol.274 , pp. 2099-2108
    • Thuku, N.R.1    Weber, B.W.2    Varsani, A.3    Sewell, T.4
  • 62
    • 23844552145 scopus 로고    scopus 로고
    • Molecular analysis of the nitrile catabolism operon of the thermophile Bacillus vallidus RAPc8
    • Cameron R.A., Sayed M. and Cowan D.A. (2005). Molecular analysis of the nitrile catabolism operon of the thermophile Bacillus vallidus RAPc8. Biochim. Biophys. Acta 1725, 35-46.
    • (2005) Biochim. Biophys. Acta , vol.1725 , pp. 35-46
    • Cameron, R.A.1    Sayed, M.2    Cowan, D.A.3
  • 64
    • 0037074923 scopus 로고    scopus 로고
    • Pseudomonas luteola lipase: A new member of the 320-residue Pseudomonas lipase family
    • Litthauer D., Ginster A. and van Eeden Skein E. (2002). Pseudomonas luteola lipase: a new member of the 320-residue Pseudomonas lipase family. Enzy. Microbiol. Technol. 30, 209-215.
    • (2002) Enzy. Microbiol. Technol , vol.30 , pp. 209-215
    • Litthauer, D.1    Ginster, A.2    van Eeden Skein, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.