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Volumn 14, Issue 5, 2005, Pages 1305-1314

Structural similarity to bridge sequence space: Finding new families on the bridges

Author keywords

Domain family; Evolution; Protein structure; Structural genomics

Indexed keywords

BACTERIAL PROTEIN;

EID: 17744375780     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.041187405     Document Type: Article
Times cited : (10)

References (57)
  • 2
    • 0036228122 scopus 로고    scopus 로고
    • Structural similarity to link sequence space: New potential superfamilies and implications for structural genomics
    • Aloy, P., Oliva, B., Querol, E., Aviles, F.X., and Russell, R.B. 2002. Structural similarity to link sequence space: New potential superfamilies and implications for structural genomics. Protein Sci. 11: 1101-1116.
    • (2002) Protein Sci. , vol.11 , pp. 1101-1116
    • Aloy, P.1    Oliva, B.2    Querol, E.3    Aviles, F.X.4    Russell, R.B.5
  • 8
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 12
    • 0036087169 scopus 로고    scopus 로고
    • SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
    • Gough, J. and Chothia, C. 2002. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res. 30: 268-272.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 268-272
    • Gough, J.1    Chothia, C.2
  • 13
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough, J., Karplus, K., Hughey, R., and Chothia, C. 2001. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol. 313: 903-919.
    • (2001) J. Mol. Biol. , vol.313 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 14
    • 0036737479 scopus 로고    scopus 로고
    • The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs
    • Griffiths-Jones, S. and Bateman, A. 2002. The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs. Bioinformatics 18: 1243-1249.
    • (2002) Bioinformatics , vol.18 , pp. 1243-1249
    • Griffiths-Jones, S.1    Bateman, A.2
  • 15
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin, N.V. 2001. Fold change in evolution of protein structures. J. Struct. Biol. 134: 167-185.
    • (2001) J. Struct. Biol. , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 16
    • 0035070578 scopus 로고    scopus 로고
    • Picasso: Generating a covering set of protein family profiles
    • Heger, A., and Holm, L. 2001. Picasso: Generating a covering set of protein family profiles. Bioinformatics 17: 272-279.
    • (2001) Bioinformatics , vol.17 , pp. 272-279
    • Heger, A.1    Holm, L.2
  • 18
    • 0029918694 scopus 로고    scopus 로고
    • The FSSP database: Fold classification based on structure-structure alignment of proteins
    • Holm, L. and Sander, C. 1996. The FSSP database: Fold classification based on structure-structure alignment of proteins. Nucleic Acids Res. 24: 206-209.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 206-209
    • Holm, L.1    Sander, C.2
  • 20
    • 0033756163 scopus 로고    scopus 로고
    • A misexpression screen identifies genes that can modulate RAS1 pathway signaling in Drosophila melanogaster
    • Huang, A.M. and Rubin, G.M. 2000. A misexpression screen identifies genes that can modulate RAS1 pathway signaling in Drosophila melanogaster. Genetics 156: 1219-1230.
    • (2000) Genetics , vol.156 , pp. 1219-1230
    • Huang, A.M.1    Rubin, G.M.2
  • 23
    • 0033846832 scopus 로고    scopus 로고
    • Improving the quality of twilight-zone alignments
    • Jaroszewski, L., Rychlewski, L., and Godzik, A. 2000. Improving the quality of twilight-zone alignments. Protein Sci. 9: 1487-1496.
    • (2000) Protein Sci. , vol.9 , pp. 1487-1496
    • Jaroszewski, L.1    Rychlewski, L.2    Godzik, A.3
  • 25
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus, K., Barrett, C., and Hughey, R. 1998. Hidden Markov models for detecting remote protein homologies. Bioinformatics 14: 846-856.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 26
    • 0034595501 scopus 로고    scopus 로고
    • Enhanced genome annotation using structural profiles in the program 3D-PSSM
    • Kelley, L.A., MacCallum, R.M., and Sternberg, M.J. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299: 499-520.
    • (2000) J. Mol. Biol. , vol.299 , pp. 499-520
    • Kelley, L.A.1    MacCallum, R.M.2    Sternberg, M.J.3
  • 30
    • 3242876311 scopus 로고    scopus 로고
    • BLAST: At the core of a powerful and diverse set of sequence analysis tools
    • McGinnis, S. and Madden, T.L. 2004. BLAST: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32: W20-W25.
    • (2004) Nucleic Acids Res. , vol.32
    • McGinnis, S.1    Madden, T.L.2
  • 31
    • 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
  • 32
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin, L.J., Bryson, K., and Jones, D.T. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16: 404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 33
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 34
    • 4444298729 scopus 로고    scopus 로고
    • Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods
    • Ohlson, T., Wallner, B., and Elofsson, A. 2004. Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods. Proteins 57: 188-197.
    • (2004) Proteins , vol.57 , pp. 188-197
    • Ohlson, T.1    Wallner, B.2    Elofsson, A.3
  • 37
    • 0036145804 scopus 로고    scopus 로고
    • A comparison of position-specific score matrices based on sequence and structure alignments
    • Panchenko, A.R. and Bryant, S.H. 2002. A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci. 11: 361-370.
    • (2002) Protein Sci. , vol.11 , pp. 361-370
    • Panchenko, A.R.1    Bryant, S.H.2
  • 38
    • 0036087098 scopus 로고    scopus 로고
    • SUPFAM - A database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: Implications for structural genomics and function annotation in genomes
    • Pandit, S.B., Gosar, D., Abhiman, S., Sujatha, S., Dixit, S.S., Mhatre, N.S., Sowdhamini, R., and Srinivasan, N. 2002. SUPFAM - A database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: Implications for structural genomics and function annotation in genomes. Nucleic Acids Res. 30: 289-293.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 289-293
    • Pandit, S.B.1    Gosar, D.2    Abhiman, S.3    Sujatha, S.4    Dixit, S.S.5    Mhatre, N.S.6    Sowdhamini, R.7    Srinivasan, N.8
  • 39
    • 0036470564 scopus 로고    scopus 로고
    • Crystal structure of reverse gyrase: Insights into the positive supercoiling of DNA
    • Rodriguez, A.C. and Stock, D. 2002. Crystal structure of reverse gyrase: Insights into the positive supercoiling of DNA. EMBO J. 21: 418-426.
    • (2002) EMBO J. , vol.21 , pp. 418-426
    • Rodriguez, A.C.1    Stock, D.2
  • 40
    • 0028300741 scopus 로고
    • Combining evolutionary information and neural networks to predict protein secondary structure
    • Rost, B. and Sander, C. 1994. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19: 55-72.
    • (1994) Proteins , vol.19 , pp. 55-72
    • Rost, B.1    Sander, C.2
  • 41
    • 0026743174 scopus 로고
    • Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
    • Russell, R.B. and Barton, G.J. 1992. Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels. Proteins 14: 309-323.
    • (1992) Proteins , vol.14 , pp. 309-323
    • Russell, R.B.1    Barton, G.J.2
  • 42
    • 0032475963 scopus 로고    scopus 로고
    • Supersites within super-folds. Binding site similarity in the absence of homology
    • Russell, R.B., Sasieni, P.D., and Sternberg, M.J. 1998. Supersites within super-folds. Binding site similarity in the absence of homology. J. Mol. Biol. 282: 903-918.
    • (1998) J. Mol. Biol. , vol.282 , pp. 903-918
    • Russell, R.B.1    Sasieni, P.D.2    Sternberg, M.J.3
  • 43
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski, L., Jaroszewski, L., Li, W., and Godzik. A. 2000. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 9: 232-241.
    • (2000) Protein Sci. , vol.9 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 44
    • 0036489460 scopus 로고    scopus 로고
    • A versatile structural domain analysis server using profile weight matrices
    • Schmidt, S., Bork, P., and Dandekar, T. 2002. A versatile structural domain analysis server using profile weight matrices. J. Chem. Inf. Comput. Sci. 42: 405-407.
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , pp. 405-407
    • Schmidt, S.1    Bork, P.2    Dandekar, T.3
  • 46
    • 0035873996 scopus 로고    scopus 로고
    • Fibroblast growth factor homologous factors are intracellular signaling proteins
    • Schoorlemmer, J. and Goldfarb, M. 2001. Fibroblast growth factor homologous factors are intracellular signaling proteins. Curr. Biol. 11: 793-797.
    • (2001) Curr. Biol. , vol.11 , pp. 793-797
    • Schoorlemmer, J.1    Goldfarb, M.2
  • 47
    • 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
  • 48
    • 0033006387 scopus 로고    scopus 로고
    • N-myc-dependent repression of ndr1, a gene identified by direct subtraction of whole mouse embryo cDNAs between wild type and N-myc mutant
    • Shimono, A., Okuda, T., and Kondoh, H. 1999. N-myc-dependent repression of ndr1, a gene identified by direct subtraction of whole mouse embryo cDNAs between wild type and N-myc mutant. Mech. Dev. 83: 39-52.
    • (1999) Mech. Dev. , vol.83 , pp. 39-52
    • Shimono, A.1    Okuda, T.2    Kondoh, H.3
  • 50
    • 0034674709 scopus 로고    scopus 로고
    • Chitin-binding proteins in invertebrates and plants comprise a common chitin-binding structural motif
    • Suetake, T., Tsuda, S., Kawabata, S., Miura, K., Iwanaga, S., Hikichi, K., Nitta, K., and Kawano, K. 2000. Chitin-binding proteins in invertebrates and plants comprise a common chitin-binding structural motif. J. Biol. Chem. 275: 17929-17932.
    • (2000) J. Biol. Chem. , vol.275 , pp. 17929-17932
    • Suetake, T.1    Tsuda, S.2    Kawabata, S.3    Miura, K.4    Iwanaga, S.5    Hikichi, K.6    Nitta, K.7    Kawano, K.8
  • 52
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd, A.E., Orengo, C.A., and Thornton, J.M. 2001. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 53
    • 0036683309 scopus 로고    scopus 로고
    • Plasticity of enzyme active sites
    • _. 2002. Plasticity of enzyme active sites. Trends Biochem. Sci. 27: 419-426.
    • (2002) Trends Biochem. Sci. , vol.27 , pp. 419-426
  • 55
    • 0033008596 scopus 로고    scopus 로고
    • Distribution of protein folds in the three superkingdoms of life
    • Wolf, Y.I., Brenner, S.E., Bash, P.A., and Koonin, E.V. 1999. Distribution of protein folds in the three superkingdoms of life. Genome Res. 9: 17-26.
    • (1999) Genome Res. , vol.9 , pp. 17-26
    • Wolf, Y.I.1    Brenner, S.E.2    Bash, P.A.3    Koonin, E.V.4
  • 56
    • 0037305974 scopus 로고    scopus 로고
    • Overview of structural genomics: From structure to function
    • Zhang, C. and Kim, S.H. 2003. Overview of structural genomics: From structure to function. Curr. Opin. Chem. Biol. 7: 28-32.
    • (2003) Curr. Opin. Chem. Biol. , vol.7 , pp. 28-32
    • Zhang, C.1    Kim, S.H.2
  • 57
    • 0034237733 scopus 로고    scopus 로고
    • Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 Å resolution: Functional implications
    • Zhang, H., Huang, K., Li, Z., Banerjei, L., Fisher, K.E., Grishin, N.V., Eisenstein, E., and Herzberg, O. 2000. Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 Å resolution: Functional implications. Proteins 40: 86-97.
    • (2000) Proteins , vol.40 , pp. 86-97
    • Zhang, H.1    Huang, K.2    Li, Z.3    Banerjei, L.4    Fisher, K.E.5    Grishin, N.V.6    Eisenstein, E.7    Herzberg, O.8


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