메뉴 건너뛰기




Volumn 385, Issue 4, 2009, Pages 1314-1329

OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries

Author keywords

chain skeleton; domain boundary; protein folding; statistical scores; structure prediction

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CONSENSUS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STATISTICAL DISTRIBUTION;

EID: 58149336791     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.10.093     Document Type: Article
Times cited : (16)

References (50)
  • 1
    • 0018782641 scopus 로고
    • Hierarchic organization of domains in globular proteins
    • Rose G.D. Hierarchic organization of domains in globular proteins. J. Mol. Biol. 134 (1979) 447-470
    • (1979) J. Mol. Biol. , vol.134 , pp. 447-470
    • Rose, G.D.1
  • 3
    • 0019588920 scopus 로고
    • Folding units in globular proteins
    • Lesk A.M., and Rose G.D. Folding units in globular proteins. Proc. Natl Acad. Sci. USA 78 (1981) 4304-4308
    • (1981) Proc. Natl Acad. Sci. USA , vol.78 , pp. 4304-4308
    • Lesk, A.M.1    Rose, G.D.2
  • 4
    • 0344527798 scopus 로고    scopus 로고
    • Structural analyses of CREB-CBP transcriptional activator-coactivator complexes by NMR spectroscopy: implications for mapping the boundaries of structural domains
    • Radhakrishnan I., Perez-Alvarado G.C., Parker D., Dyson H.J., Montminy M.R., and Wright P.E. Structural analyses of CREB-CBP transcriptional activator-coactivator complexes by NMR spectroscopy: implications for mapping the boundaries of structural domains. J. Mol. Biol. 287 (1999) 859-865
    • (1999) J. Mol. Biol. , vol.287 , pp. 859-865
    • Radhakrishnan, I.1    Perez-Alvarado, G.C.2    Parker, D.3    Dyson, H.J.4    Montminy, M.R.5    Wright, P.E.6
  • 6
    • 33746338567 scopus 로고    scopus 로고
    • Partitioning protein structures into domains: why is it so difficult?
    • Holland T.A., Veretnik S., Shindyalov I.N., and Bourne P.E. Partitioning protein structures into domains: why is it so difficult?. J. Mol. Biol. 361 (2006) 562-590
    • (2006) J. Mol. Biol. , vol.361 , pp. 562-590
    • Holland, T.A.1    Veretnik, S.2    Shindyalov, I.N.3    Bourne, P.E.4
  • 7
    • 0033753811 scopus 로고    scopus 로고
    • Domain size distributions can predict domain boundaries
    • Wheelan S.J., Marchler-Bauer A., and Bryant S.H. Domain size distributions can predict domain boundaries. Bioinformatics 16 (2000) 613-618
    • (2000) Bioinformatics , vol.16 , pp. 613-618
    • Wheelan, S.J.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 8
    • 0037460953 scopus 로고    scopus 로고
    • DomCut: prediction of inter-domain linker regions in amino acid sequences
    • Suyama M., and Ohara O. DomCut: prediction of inter-domain linker regions in amino acid sequences. Bioinformatics 19 (2003) 673-674
    • (2003) Bioinformatics , vol.19 , pp. 673-674
    • Suyama, M.1    Ohara, O.2
  • 9
    • 0036893072 scopus 로고    scopus 로고
    • Rapid protein domain assignment from amino acid sequence using predicted secondary structure
    • Marsden R.L., McGuffin L.J., and Jones D.T. Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci. 11 (2002) 2814-2824
    • (2002) Protein Sci. , vol.11 , pp. 2814-2824
    • Marsden, R.L.1    McGuffin, L.J.2    Jones, D.T.3
  • 10
    • 32144434539 scopus 로고    scopus 로고
    • SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles
    • Gewehr J.E., and Zimmer R. SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics 22 (2006) 181-187
    • (2006) Bioinformatics , vol.22 , pp. 181-187
    • Gewehr, J.E.1    Zimmer, R.2
  • 11
    • 33947385412 scopus 로고    scopus 로고
    • Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index
    • Sikder A.R., and Zomaya A.Y. Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index. BMC Bioinformatics 7 Suppl 5 (2006) S6
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 5
    • Sikder, A.R.1    Zomaya, A.Y.2
  • 12
    • 0036288851 scopus 로고    scopus 로고
    • Characterization and prediction of linker sequences of multi-domain proteins by a neural network
    • Miyazaki S., Kuroda Y., and Yokoyama S. Characterization and prediction of linker sequences of multi-domain proteins by a neural network. J. Struct. Funct. Genomics 2 (2002) 37-51
    • (2002) J. Struct. Funct. Genomics , vol.2 , pp. 37-51
    • Miyazaki, S.1    Kuroda, Y.2    Yokoyama, S.3
  • 13
    • 23144465987 scopus 로고    scopus 로고
    • SCRATCH: a protein structure and structural feature prediction server
    • Cheng J., Randall A.Z., Sweredoski M.J., and Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. 33 (2005) W72-W76
    • (2005) Nucleic Acids Res. , vol.33
    • Cheng, J.1    Randall, A.Z.2    Sweredoski, M.J.3    Baldi, P.4
  • 14
    • 3042810008 scopus 로고    scopus 로고
    • Sequence-based prediction of protein domains
    • Liu J., and Rost B. Sequence-based prediction of protein domains. Nucleic Acids Res. 32 (2004) 3522-3530
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3522-3530
    • Liu, J.1    Rost, B.2
  • 15
    • 17844363963 scopus 로고    scopus 로고
    • PPRODO: prediction of protein domain boundaries using neural networks
    • Sim J., Kim S.Y., and Lee J. PPRODO: prediction of protein domain boundaries using neural networks. Proteins 59 (2005) 627-632
    • (2005) Proteins , vol.59 , pp. 627-632
    • Sim, J.1    Kim, S.Y.2    Lee, J.3
  • 16
    • 45249093424 scopus 로고    scopus 로고
    • DomNet: protein domain boundary prediction using enhanced general regression network and new profiles
    • Yoo P.D., Sikder A.R., Taheri J., Zhou B.B., and Zomaya A.Y. DomNet: protein domain boundary prediction using enhanced general regression network and new profiles. IEEE Trans. Nanobiosci. 7 (2008) 172-181
    • (2008) IEEE Trans. Nanobiosci. , vol.7 , pp. 172-181
    • Yoo, P.D.1    Sikder, A.R.2    Taheri, J.3    Zhou, B.B.4    Zomaya, A.Y.5
  • 17
    • 33747836566 scopus 로고    scopus 로고
    • KemaDom: a Web server for domain prediction using kernel machine with local context
    • Chen L., Wang W., Ling S., Jia C., and Wang F. KemaDom: a Web server for domain prediction using kernel machine with local context. Nucleic Acids Res. 34 (2006) W158-W163
    • (2006) Nucleic Acids Res. , vol.34
    • Chen, L.1    Wang, W.2    Ling, S.3    Jia, C.4    Wang, F.5
  • 18
    • 3142680264 scopus 로고    scopus 로고
    • Automatic prediction of protein domains from sequence information using a hybrid learning system
    • Nagarajan N., and Yona G. Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics 20 (2004) 1335-1360
    • (2004) Bioinformatics , vol.20 , pp. 1335-1360
    • Nagarajan, N.1    Yona, G.2
  • 19
    • 33745101459 scopus 로고    scopus 로고
    • DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks
    • Cheng J., Sweredoski M.J., and Baldi P. DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks. Data Min. Knowl. Discov. 13 (2006) 1-10
    • (2006) Data Min. Knowl. Discov. , vol.13 , pp. 1-10
    • Cheng, J.1    Sweredoski, M.J.2    Baldi, P.3
  • 20
    • 21744461895 scopus 로고    scopus 로고
    • Armadillo: domain boundary prediction by amino acid composition
    • Dumontier M., Yao R., Feldman H.J., and Hogue C.W. Armadillo: domain boundary prediction by amino acid composition. J. Mol. Biol. 350 (2005) 1061-1073
    • (2005) J. Mol. Biol. , vol.350 , pp. 1061-1073
    • Dumontier, M.1    Yao, R.2    Feldman, H.J.3    Hogue, C.W.4
  • 21
    • 34247560816 scopus 로고    scopus 로고
    • Prediction of number and position of domain boundaries in multi-domain proteins by use of amino acid sequence alone
    • Dovidchenko N.V., Yu Lobanov M., and Galzitskaya O.V. Prediction of number and position of domain boundaries in multi-domain proteins by use of amino acid sequence alone. Curr. Protein Pept. Sci. 8 (2007) 189-195
    • (2007) Curr. Protein Pept. Sci. , vol.8 , pp. 189-195
    • Dovidchenko, N.V.1    Yu Lobanov, M.2    Galzitskaya, O.V.3
  • 22
    • 0036306348 scopus 로고    scopus 로고
    • SnapDRAGON: a method to delineate protein structural domains from sequence data
    • George R.A., and Heringa J. SnapDRAGON: a method to delineate protein structural domains from sequence data. J. Mol. Biol. 316 (2002) 839-851
    • (2002) J. Mol. Biol. , vol.316 , pp. 839-851
    • George, R.A.1    Heringa, J.2
  • 23
    • 30344438515 scopus 로고    scopus 로고
    • Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM
    • Kim D.E., Chivian D., Malmstrom L., and Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins 61 Suppl 7 (2005) 193-200
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 193-200
    • Kim, D.E.1    Chivian, D.2    Malmstrom, L.3    Baker, D.4
  • 24
    • 0029097099 scopus 로고
    • Global fold determination from a small number of distance restraints
    • Aszodi A., Gradwell M.J., and Taylor W.R. Global fold determination from a small number of distance restraints. J. Mol. Biol. 251 (1995) 308-326
    • (1995) J. Mol. Biol. , vol.251 , pp. 308-326
    • Aszodi, A.1    Gradwell, M.J.2    Taylor, W.R.3
  • 25
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • Simons K.T., Ruczinski I., Kooperberg C., Fox B.A., Bystroff C., and Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34 (1999) 82-95
    • (1999) Proteins , vol.34 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 26
    • 34547591340 scopus 로고    scopus 로고
    • DOMAC: an accurate, hybrid protein domain prediction server
    • Cheng J. DOMAC: an accurate, hybrid protein domain prediction server. Nucleic Acids Res. 35 (2007) W354-W356
    • (2007) Nucleic Acids Res. , vol.35
    • Cheng, J.1
  • 27
    • 20844435796 scopus 로고    scopus 로고
    • Meta-DP: domain prediction meta-server
    • Saini H.K., and Fischer D. Meta-DP: domain prediction meta-server. Bioinformatics 21 (2005) 2917-2920
    • (2005) Bioinformatics , vol.21 , pp. 2917-2920
    • Saini, H.K.1    Fischer, D.2
  • 28
    • 34247566179 scopus 로고    scopus 로고
    • Computer-assisted protein domain boundary prediction using the Dom-Pred server
    • Bryson K., Cozzetto D., and Jones D.T. Computer-assisted protein domain boundary prediction using the Dom-Pred server. Curr. Protein Pept. Sci. 8 (2007) 181-188
    • (2007) Curr. Protein Pept. Sci. , vol.8 , pp. 181-188
    • Bryson, K.1    Cozzetto, D.2    Jones, D.T.3
  • 29
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292 (1999) 195-202
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 30
    • 58149342116 scopus 로고    scopus 로고
    • Guoguang, L. (1999). DOMID. Version 1.0 Mar-15-1999. Karolinska Institute. Version 2.5 Nov-9-1999 Lund Univ.
    • Guoguang, L. (1999). DOMID. Version 1.0 Mar-15-1999. Karolinska Institute. Version 2.5 Nov-9-1999 Lund Univ.
  • 31
    • 0032951163 scopus 로고    scopus 로고
    • Protein structural domain identification
    • Taylor W.R. Protein structural domain identification. Protein Eng. 12 (1999) 203-216
    • (1999) Protein Eng. , vol.12 , pp. 203-216
    • Taylor, W.R.1
  • 34
    • 0037377548 scopus 로고    scopus 로고
    • Prediction of protein domain boundaries from sequence alone
    • Galzitskaya O.V., and Melnik B.S. Prediction of protein domain boundaries from sequence alone. Protein Sci. 12 (2003) 696-701
    • (2003) Protein Sci. , vol.12 , pp. 696-701
    • Galzitskaya, O.V.1    Melnik, B.S.2
  • 35
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 38
    • 0033011876 scopus 로고    scopus 로고
    • Protein structure comparison using iterated double dynamic programming
    • Taylor W.R. Protein structure comparison using iterated double dynamic programming. Protein Sci. 8 (1999) 654-665
    • (1999) Protein Sci. , vol.8 , pp. 654-665
    • Taylor, W.R.1
  • 39
    • 36749014942 scopus 로고    scopus 로고
    • Assessment of predictions submitted for the CASP7 domain prediction category
    • Tress M., Cheng J., Baldi P., Joo K., Lee J., Seo J.H., et al. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins 69 Suppl 8 (2007) 137-151
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 137-151
    • Tress, M.1    Cheng, J.2    Baldi, P.3    Joo, K.4    Lee, J.5    Seo, J.H.6
  • 42
    • 0034491038 scopus 로고    scopus 로고
    • Protein domain decomposition using a graph-theoretic approach
    • Xu Y., Xu D., and Gabow H.N. Protein domain decomposition using a graph-theoretic approach. Bioinformatics 16 (2000) 1091-1104
    • (2000) Bioinformatics , vol.16 , pp. 1091-1104
    • Xu, Y.1    Xu, D.2    Gabow, H.N.3
  • 43
    • 0028838717 scopus 로고
    • Threading a database of protein cores
    • Madej T., Gibrat J.F., and Bryant S.H. Threading a database of protein cores. Proteins 23 (1995) 356-369
    • (1995) Proteins , vol.23 , pp. 356-369
    • Madej, T.1    Gibrat, J.F.2    Bryant, S.H.3
  • 45
    • 0028290005 scopus 로고
    • Parser for protein folding units
    • Holm L., and Sander C. Parser for protein folding units. Proteins 19 (1994) 256-268
    • (1994) Proteins , vol.19 , pp. 256-268
    • Holm, L.1    Sander, C.2
  • 46
    • 20444490870 scopus 로고    scopus 로고
    • Determining protein topology from skeletons of secondary structures
    • Wu Y., Chen M., Lu M., Wang Q., and Ma J. Determining protein topology from skeletons of secondary structures. J. Mol. Biol. 350 (2005) 571-586
    • (2005) J. Mol. Biol. , vol.350 , pp. 571-586
    • Wu, Y.1    Chen, M.2    Lu, M.3    Wang, Q.4    Ma, J.5
  • 47
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G., and Dunbrack Jr. R.L. PISCES: a protein sequence culling server. Bioinformatics 19 (2003) 1589-1591
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 48
    • 0002087305 scopus 로고    scopus 로고
    • Hard convex body fluids
    • Prigogine I., and Rice S.A. (Eds), John Wiley Sons, Inc., New York, NY
    • Allen M.P., Evans G.T., Frenkel D., and Mulder B.M. Hard convex body fluids. In: Prigogine I., and Rice S.A. (Eds). Advances in Chemical Physics 86 (2007), John Wiley Sons, Inc., New York, NY 1-166
    • (2007) Advances in Chemical Physics , vol.86 , pp. 1-166
    • Allen, M.P.1    Evans, G.T.2    Frenkel, D.3    Mulder, B.M.4
  • 49
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • Bahar I., and Jernigan R.L. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266 (1997) 195-214
    • (1997) J. Mol. Biol. , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 50
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith T.F., and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.