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Volumn 2, Issue 1, 2004, Pages 61-75

Statistical and visual morph movie analysis of crystallographic mutant selection bias in protein mutation resource data

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

EID: 3242879631     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720004000478     Document Type: Article
Times cited : (1)

References (43)
  • 1
    • 0033584187 scopus 로고    scopus 로고
    • "Discovery of a highly potent, functionally-selective muscarinic M1 agonist, WAY-132983 using rational drug design and receptor modelling"
    • A. L. Sabb, G. M. Husbands, J. Tokolics, R. P. Stein, R. P. Tasse, C. A. Boast, J. A. Moyer and M. Abou-Gharbia, "Discovery of a highly potent, functionally-selective muscarinic M1 agonist, WAY-132983 using rational drug design and receptor modelling," Bioorg. Med. Chem. Lett. 9, 1895-1900 (1999).
    • (1999) Bioorg. Med. Chem. Lett. , vol.9 , pp. 1895-1900
    • Sabb, A.L.1    Husbands, G.M.2    Tokolics, J.3    Stein, R.P.4    Tasse, R.P.5    Boast, C.A.6    Moyer, J.A.7    Abou-Gharbia, M.8
  • 2
    • 0028168137 scopus 로고
    • "Modelling the structure of the calcitonin gene-related peptide"
    • J. M. Hakala and M. Vihinen, "Modelling the structure of the calcitonin gene-related peptide," Protein Eng. 7, 1069-1075 (1994).
    • (1994) Protein Eng. , vol.7 , pp. 1069-1075
    • Hakala, J.M.1    Vihinen, M.2
  • 3
    • 0028276364 scopus 로고
    • "Homology modelling of the dihydrofolate reductase-thymidylate synthase bifunctional enzyme of Leishmania major, a potential target for rational drug design in leishmaniasis"
    • J. H. McKie, "Homology modelling of the dihydrofolate reductase-thymidylate synthase bifunctional enzyme of Leishmania major, a potential target for rational drug design in leishmaniasis," Drug Des. Discov. 11, 269-288 (1994).
    • (1994) Drug Des. Discov. , vol.11 , pp. 269-288
    • McKie, J.H.1
  • 4
    • 0025398721 scopus 로고
    • "WHAT IF: A molecular modeling and drug design program"
    • G. Vriend, "WHAT IF: A molecular modeling and drug design program," J. Mol. Graph. 8, 52-56 (1990).
    • (1990) J. Mol. Graph. , vol.8 , pp. 52-56
    • Vriend, G.1
  • 5
    • 0028856785 scopus 로고
    • "Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications"
    • A. R. Fersht, "Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications," Proc. Natl. Acad. Sci. USA 92, 10869-10873 (1995).
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 10869-10873
    • Fersht, A.R.1
  • 6
    • 0029115970 scopus 로고
    • "Optimal local propensities for model proteins"
    • S. Govindarajan and R. A. Goldstein, "Optimal local propensities for model proteins," Proteins 22, 413-418 (1995).
    • (1995) Proteins , vol.22 , pp. 413-418
    • Govindarajan, S.1    Goldstein, R.A.2
  • 7
    • 0030604696 scopus 로고    scopus 로고
    • "Local interactions dominate folding in a simple protein model"
    • R. Unger and J. Moult, "Local interactions dominate folding in a simple protein model," J. Mol. Biol. 259, 988-994 (1996).
    • (1996) J. Mol. Biol. , vol.259 , pp. 988-994
    • Unger, R.1    Moult, J.2
  • 9
    • 0008600208 scopus 로고    scopus 로고
    • "TinyGRAP database: A bioinformatics tool to mine G-protein-coupled receptor mutant data"
    • I.J. AP
    • M. W. Beukers, I. Kristiansen, I. J. AP and I. Edvardsen, "TinyGRAP database: a bioinformatics tool to mine G-protein-coupled receptor mutant data," Trends Pharmacol. Sci. 20, 475-477 (1999).
    • (1999) Trends Pharmacol. Sci. , vol.20 , pp. 475-477
    • Beukers, M.W.1    Kristiansen, I.2    Edvardsen, I.3
  • 10
    • 0029845242 scopus 로고    scopus 로고
    • "A database of mutants and effects of site-directed mutagenesis experiments on G protein-coupled receptors"
    • K. Kristiansen, S. G. Dahl and O. Edvardsen, "A database of mutants and effects of site-directed mutagenesis experiments on G protein-coupled receptors," Proteins 26, 81-94 (1996).
    • (1996) Proteins , vol.26 , pp. 81-94
    • Kristiansen, K.1    Dahl, S.G.2    Edvardsen, O.3
  • 11
    • 0002570174 scopus 로고    scopus 로고
    • "Computerization of mutant data: The tinyGRAP mutant database"
    • I. Edvardsen and K. Kristiansen, "Computerization of mutant data: the tinyGRAP mutant database," 7TM Journal 6, 1-6 (1997).
    • (1997) 7TM Journal , vol.6 , pp. 1-6
    • Edvardsen, I.1    Kristiansen, K.2
  • 15
    • 0036084144 scopus 로고    scopus 로고
    • "ProTherm, Thermodynamic database for proteins and mutants: Developments in version 3.0"
    • M. M. Gromiha, H. Uedaira, J. An, S. Selvaraj, P. Prabakaran and A. Sarai, "ProTherm, Thermodynamic database for proteins and mutants: Developments in version 3.0," Nucleic Acids Res. 30, 301-302 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 301-302
    • Gromiha, M.M.1    Uedaira, H.2    An, J.3    Selvaraj, S.4    Prabakaran, P.5    Sarai, A.6
  • 16
    • 3242891161 scopus 로고    scopus 로고
    • "The protein mutant resource: A tool for protein engineering"
    • Manuscript in preparation
    • W. G. Krebs, T. M. Nair and P. E. Bourne, "The protein mutant resource: A tool for protein engineering," Manuscript in preparation (2003).
    • (2003)
    • Krebs, W.G.1    Nair, T.M.2    Bourne, P.E.3
  • 18
    • 0031715982 scopus 로고    scopus 로고
    • "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path"
    • I. N. Shindyalov and P. E. Bourne, "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path," Protein Eng. 11, 739-747 (1998).
    • (1998) Protein Eng. , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 20
    • 2442657797 scopus 로고    scopus 로고
    • "Statistically Rigorous Automated Protein Annotation"
    • vol. in press
    • W. G. Krebs and P. E. Bourne, "Statistically Rigorous Automated Protein Annotation," Bioinformatics, vol. in press (2004).
    • (2004) Bioinformatics
    • Krebs, W.G.1    Bourne, P.E.2
  • 21
    • 0036606878 scopus 로고    scopus 로고
    • "Genome annotation techniques: New approaches and challenges"
    • A. G. Rust, E. Mongin and E. Birney, "Genome annotation techniques: New approaches and challenges," Drug Discov. Today 7, S70-S76 (2002).
    • (2002) Drug Discov. Today , vol.7
    • Rust, A.G.1    Mongin, E.2    Birney, E.3
  • 22
    • 1842743412 scopus 로고    scopus 로고
    • "Automated annotation of keywords for proteins related to mycoplasmataceae using machine learning techniques"
    • A. L. Bazzan, P. M. Engel, L. F. Schroeder and S. C. Da Silva, "Automated annotation of keywords for proteins related to mycoplasmataceae using machine learning techniques," Bioinformatics 18(Suppl. 2), S35-S43, (2002).
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 2
    • Bazzan, A.L.1    Engel, P.M.2    Schroeder, L.F.3    Da Silva, S.C.4
  • 25
    • 84960461548 scopus 로고    scopus 로고
    • "Studying protein flexibility in a statistical framework: Tools and databases for analyzing structures and approaches for mapping this onto sequences"
    • W. Krebs, J. Tsai, V. Alexandrov, J. Junker, R. Jansen and M. Gerstein, "Studying protein flexibility in a statistical framework: Tools and databases for analyzing structures and approaches for mapping this onto sequences," Methods Enzymol. 374 (2003).
    • (2003) Methods Enzymol. , vol.374
    • Krebs, W.1    Tsai, J.2    Alexandrov, V.3    Junker, J.4    Jansen, R.5    Gerstein, M.6
  • 26
    • 0034655949 scopus 로고    scopus 로고
    • "The morph server: A standardized system for analyzing and visualizing macromolecular motions in a database framework"
    • W. G. Krebs and M. Gerstein, "The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework," Nucleic Acids Res. 28, 1665-1675 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1665-1675
    • Krebs, W.G.1    Gerstein, M.2
  • 27
    • 0037246863 scopus 로고    scopus 로고
    • "MolMovDB: Analysis and visualization of conformational change and structural flexibility"
    • N. Echols, D. Milburn and M. Gerstein, "MolMovDB: analysis and visualization of conformational change and structural flexibility," Nucleic Acids Res. 31, 478-482 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 478-482
    • Echols, N.1    Milburn, D.2    Gerstein, M.3
  • 28
    • 0032530836 scopus 로고    scopus 로고
    • "A database of macromolecular movements"
    • M. Gerstein and W. Krebs, "A database of macromolecular movements," Nucleic Acids Res. 26, 4280 (1998).
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4280
    • Gerstein, M.1    Krebs, W.2
  • 30
    • 0030010970 scopus 로고    scopus 로고
    • "Entrez: Molecular biology database and retrieval system"
    • G. D. Schuler, J. A. Epstein, H. Ohkawa and J. A. Kans, "Entrez: Molecular biology database and retrieval system," Methods Enzymol. 266, 141-162 (1996).
    • (1996) Methods Enzymol. , vol.266 , pp. 141-162
    • Schuler, G.D.1    Epstein, J.A.2    Ohkawa, H.3    Kans, J.A.4
  • 32
    • 0035072551 scopus 로고    scopus 로고
    • "Clustering of highly homologous sequences to reduce the size of large protein databases"
    • W. Li, L. Jaroszewski and A. Godzik, "Clustering of highly homologous sequences to reduce the size of large protein databases," Bioinformatics 17, 282-283 (2001).
    • (2001) Bioinformatics , vol.17 , pp. 282-283
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 33
    • 0031829372 scopus 로고    scopus 로고
    • "Removing near-neighbour redundancy from large protein sequence collections"
    • L. Holm and C. Sander, "Removing near-neighbour redundancy from large protein sequence collections," Bioinformatics 14, 423-429 (1998).
    • (1998) Bioinformatics , vol.14 , pp. 423-429
    • Holm, L.1    Sander, C.2
  • 35
    • 0036721233 scopus 로고    scopus 로고
    • "Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic"
    • W. G. Krebs, V. Alexandrov, C. A. Wilson, N. Echols, H. Yu and M. Gerstein, "Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic," Proteins 48, 682-695 (2002).
    • (2002) Proteins , vol.48 , pp. 682-695
    • Krebs, W.G.1    Alexandrov, V.2    Wilson, C.A.3    Echols, N.4    Yu, H.5    Gerstein, M.6
  • 36
    • 0000987560 scopus 로고    scopus 로고
    • "Studying macromolecular motions in a database framework: From structure to sequence"
    • M. F. Thorpe and P. M. Duxbury, Eds. New York: Kluwer Academic/Plenum press
    • M. B. Gerstein, R. Jansen, T. Johnson, B. Park and W. Krebs, "Studying macromolecular motions in a database framework: From structure to sequence," in Rigidity Theory and Applications, Fundamental Materials Science, M. F. Thorpe and P. M. Duxbury, Eds. New York: Kluwer Academic/Plenum press (1999), pp. 401-442.
    • (1999) Rigidity Theory and Applications, Fundamental Materials Science , pp. 401-442
    • Gerstein, M.B.1    Jansen, R.2    Johnson, T.3    Park, B.4    Krebs, W.5
  • 37
    • 0343308710 scopus 로고    scopus 로고
    • "Protein Explorer"
    • (software package)
    • E. Martz, "Protein Explorer (software package)," http://www.umass.edu/microbio/chime/explorer/index.htm (1999).
    • (1999)
    • Martz, E.1
  • 38
    • 0021604916 scopus 로고
    • "Mechanisms of domain closure in proteins"
    • A. M. Lesk and C. Chothia, "Mechanisms of domain closure in proteins," J. Mol. Biol. 174, 175-191 (1984).
    • (1984) J. Mol. Biol. , vol.174 , pp. 175-191
    • Lesk, A.M.1    Chothia, C.2
  • 39
    • 0025272240 scopus 로고
    • "Rapid and sensitive sequence comparison with FASTP and FASTA"
    • W. R. Pearson, "Rapid and sensitive sequence comparison with FASTP and FASTA," Methods Enzymol. 183, 63-98 (1990).
    • (1990) Methods Enzymol. , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 40
    • 0028983795 scopus 로고
    • "Crystal structure of Thermus aquaticus DNA polymerase"
    • Y. Kim, S. H. Eom, J. Wang, D. S. Lee, S. W. Suh and T. A. Steitz, "Crystal structure of Thermus aquaticus DNA polymerase," Nature 376, 612-616 (1995).
    • (1995) Nature , vol.376 , pp. 612-616
    • Kim, Y.1    Eom, S.H.2    Wang, J.3    Lee, D.S.4    Suh, S.W.5    Steitz, T.A.6
  • 41
    • 0021099424 scopus 로고
    • "Three-dimensional structure of isonicotinimidylated liver alcohol dehydrogenase"
    • B. V. Plapp, H. Eklund, T. A. Jones and C. I. Branden, "Three-dimensional structure of isonicotinimidylated liver alcohol dehydrogenase," J. Biol. Chem. 258, 5537-5547 (1983).
    • (1983) J. Biol. Chem. , vol.258 , pp. 5537-5547
    • Plapp, B.V.1    Eklund, H.2    Jones, T.A.3    Branden, C.I.4
  • 42
    • 0028157608 scopus 로고
    • "Crystallographic studies of two alcohol dehydrogenase-bound analogues of thiazole-4-carboxamide adenine dinucleotide (TAD), the active anabolite of the antitumor agent tiazofurin"
    • H. Li, W. H. Hallows, J. S. Punzi, V. E. Marquez, H. L. Carrell, K. W. Pankiewicz, K. A. Watanabe and B. M. Goldstein, "Crystallographic studies of two alcohol dehydrogenase-bound analogues of thiazole-4-carboxamide adenine dinucleotide (TAD), the active anabolite of the antitumor agent tiazofurin," Biochemistry 33, 23-32 (1994).
    • (1994) Biochemistry , vol.33 , pp. 23-32
    • Li, H.1    Hallows, W.H.2    Punzi, J.S.3    Marquez, V.E.4    Carrell, H.L.5    Pankiewicz, K.W.6    Watanabe, K.A.7    Goldstein, B.M.8
  • 43
    • 0028158008 scopus 로고
    • "Rapid crystallization of T4 lysozyme by intermolecular disulfide cross-linking"
    • D. W. Heinz and B. W. Matthews, "Rapid crystallization of T4 lysozyme by intermolecular disulfide cross-linking," Protein Eng. 7, 301-307 (1994).
    • (1994) Protein Eng. , vol.7 , pp. 301-307
    • Heinz, D.W.1    Matthews, B.W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.