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Volumn 40, Issue D1, 2012, Pages

IndelFR: A database of indels in protein structures and their flanking regions

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; ASPARAGINE; ASPARTIC ACID; GLUTAMIC ACID; GLUTAMINE; HISTIDINE; LYSINE; SERINE; THREONINE;

EID: 84862155641     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1107     Document Type: Article
Times cited : (15)

References (31)
  • 1
    • 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
  • 2
    • 78650800495 scopus 로고    scopus 로고
    • The combined effects of amino acid substitutions and indels on the evolution of structure within protein families
    • Zhang,Z., Wang,Y., Wang,L. and Gao,P. (2010) The combined effects of amino acid substitutions and indels on the evolution of structure within protein families. PLoS ONE, 5, e14316.
    • (2010) PLoS ONE , vol.5
    • Zhang, Z.1    Wang, Y.2    Wang, L.3    Gao, P.4
  • 3
    • 67649369319 scopus 로고    scopus 로고
    • Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria
    • Chen,J.Q., Wu,Y., Yang,H., Bergelson,J., Kreitman,M. and Tian,D. (2009) Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol. Biol. Evol., 26, 1523-1531.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 1523-1531
    • Chen, J.Q.1    Wu, Y.2    Yang, H.3    Bergelson, J.4    Kreitman, M.5    Tian, D.6
  • 5
    • 0029584496 scopus 로고
    • Trinucleotide repeat expansion and human disease
    • Ashley,C.T. Jr and Warren,S.T. (1995) Trinucleotide repeat expansion and human disease. Annu. Rev. Genet., 29, 703-728.
    • (1995) Annu. Rev. Genet. , vol.29 , pp. 703-728
    • Ashley Jr., C.T.1    Warren, S.T.2
  • 6
    • 0029616734 scopus 로고
    • Cystic fibrosis: Genotypic and phenotypic variations
    • Zielenski,J. and Tsui,L.C. (1995) Cystic fibrosis: genotypic and phenotypic variations. Annu. Rev. Genet., 29, 777-807. (Pubitemid 26005359)
    • (1995) Annual Review of Genetics , vol.29 , pp. 777-807
    • Zielenski, J.1    Tsui, L.-C.2
  • 7
    • 0034094873 scopus 로고    scopus 로고
    • Glutamine repeats and neurodegeneration
    • DOI 10.1146/annurev.neuro.23.1.217
    • Zoghbi,H.Y. and Orr,H.T. (2000) Glutamine repeats and neurodegeneration. Annu. Rev. Neurosci., 23, 217-247. (Pubitemid 30350043)
    • (2000) Annual Review of Neuroscience , vol.23 , pp. 217-247
    • Zoghbi, H.Y.1    Orr, H.T.2
  • 8
    • 0036569940 scopus 로고    scopus 로고
    • Mutations at coding repeat sequences in mismatch repair-deficient human cancers: Toward a new concept of target genes for instability
    • Duval,A. and Hamelin,R. (2002) Mutations at coding repeat sequences in mismatch repair-deficient human cancers: toward a new concept of target genes for instability. Cancer Res., 62, 2447-2454. (Pubitemid 34462716)
    • (2002) Cancer Research , vol.62 , Issue.9 , pp. 2447-2454
    • Duval, A.1    Hamelin, R.2
  • 9
    • 0031794743 scopus 로고    scopus 로고
    • Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes
    • Gupta,R.S. (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol. Mol. Biol. Rev., 62, 1435-1491.
    • (1998) Microbiol. Mol. Biol. Rev. , vol.62 , pp. 1435-1491
    • Gupta, R.S.1
  • 10
    • 77149149384 scopus 로고    scopus 로고
    • Signature proteins for the major clades of Cyanobacteria
    • Gupta,R.S. and Mathews,D.W. (2010) Signature proteins for the major clades of Cyanobacteria. BMC Evol. Biol., 10, 24.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 24
    • Gupta, R.S.1    Mathews, D.W.2
  • 11
    • 47249093329 scopus 로고    scopus 로고
    • Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins
    • Hsing,M. and Cherkasov,A. (2008) Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins. BMC Bioinform., 9, 293.
    • (2008) BMC Bioinform. , vol.9 , pp. 293
    • Hsing, M.1    Cherkasov, A.2
  • 12
    • 0026566796 scopus 로고
    • Analysis of insertions/deletions in protein structures
    • Pascarella,S. and Argos,P. (1992) Analysis of insertions/deletions in protein structures. J. Mol. Biol., 224, 461-471.
    • (1992) J. Mol. Biol. , vol.224 , pp. 461-471
    • Pascarella, S.1    Argos, P.2
  • 13
    • 0027483434 scopus 로고
    • Empirical and structural models for insertions and deletions in the divergent evolution of proteins
    • DOI 10.1006/jmbi.1993.1105
    • Benner,S.A., Cohen,M.A. and Gonnet,G.H. (1993) Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J. Mol. Biol., 229, 1065-1082. (Pubitemid 23091821)
    • (1993) Journal of Molecular Biology , vol.229 , Issue.4 , pp. 1065-1082
    • Benner, S.A.1    Cohen, M.A.2    Gonnet, G.H.3
  • 14
    • 0036601353 scopus 로고    scopus 로고
    • Trends in protein evolution inferred from sequence and structure analysis
    • DOI 10.1016/S0959-440X(02)00334-2
    • Aravind,L., Mazumder,R., Vasudevan,S. and Koonin,E.V. (2002) Trends in protein evolution inferred from sequence and structure analysis. Curr. Opin. Struct. Biol., 12, 392-399. (Pubitemid 34804623)
    • (2002) Current Opinion in Structural Biology , vol.12 , Issue.3 , pp. 392-399
    • Aravind, L.1    Mazumder, R.2    Vasudevan, S.3    Koonin, E.V.4
  • 15
    • 1342310533 scopus 로고    scopus 로고
    • Rapid evolution in conformational space: A study of loop regions in a ubiquitous GTP binding domain
    • DOI 10.1110/ps.03299804
    • Blouin,C., Butt,D. and Roger,A.J. (2004) Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain. Protein Sci., 13, 608-616. (Pubitemid 38252557)
    • (2004) Protein Science , vol.13 , Issue.3 , pp. 608-616
    • Blouin, C.1    Butt, D.2    Roger, A.J.3
  • 17
    • 34547101942 scopus 로고    scopus 로고
    • Relationship between insertion/deletion (indel) frequency of proteins and essentiality
    • Chan,S.K., Hsing,M., Hormozdiari,F. and Cherkasov,A. (2007) Relationship between insertion/deletion (indel) frequency of proteins and essentiality. BMC Bioinformatics, 8, 227.
    • (2007) BMC Bioinformatics , vol.8 , pp. 227
    • Chan, S.K.1    Hsing, M.2    Hormozdiari, F.3    Cherkasov, A.4
  • 18
    • 0037423828 scopus 로고    scopus 로고
    • How the global structure of protein interaction networks evolves
    • Wagner,A. (2003) How the global structure of protein interaction networks evolves. Proc. Biol. Sci., 270, 457-466.
    • (2003) Proc. Biol. Sci. , vol.270 , pp. 457-466
    • Wagner, A.1
  • 19
    • 51649094321 scopus 로고    scopus 로고
    • Built-in loops allow versatility in domain-domain interactions: Lessons from self-interacting domains
    • Akiva,E., Itzhaki,Z. and Margalit,H. (2008) Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. Proc. Natl Acad. Sci. USA, 105, 13292-13297.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 13292-13297
    • Akiva, E.1    Itzhaki, Z.2    Margalit, H.3
  • 20
    • 78650537920 scopus 로고    scopus 로고
    • Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states
    • Hashimoto,K. and Panchenko,A.R. (2010) Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states. Proc. Natl Acad. Sci. USA, 107, 20352-20357.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 20352-20357
    • Hashimoto, K.1    Panchenko, A.R.2
  • 21
    • 33745727120 scopus 로고    scopus 로고
    • Structural Diversity of Domain Superfamilies in the CATH Database
    • DOI 10.1016/j.jmb.2006.05.035, PII S0022283606006176
    • Reeves,G.A., Dallman,T.J., Redfern,O.C., Akpor,A. and Orengo,C.A. (2006) Structural diversity of domain superfamilies in the CATH database. J. Mol. Biol., 360, 725-741. (Pubitemid 43996855)
    • (2006) Journal of Molecular Biology , vol.360 , Issue.3 , pp. 725-741
    • Reeves, G.A.1    Dallman, T.J.2    Redfern, O.C.3    Akpor, A.4    Orengo, C.A.5
  • 22
    • 38849191693 scopus 로고    scopus 로고
    • Insertions and the emergence of novel protein structure: A structure-based phylogenetic study of insertions
    • Jiang,H. and Blouin,C. (2007) Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions. BMC Bioinformatics, 8, 444.
    • (2007) BMC Bioinformatics , vol.8 , pp. 444
    • Jiang, H.1    Blouin, C.2
  • 24
    • 70349934568 scopus 로고    scopus 로고
    • Genomewide association between insertions/deletions and the nucleotide diversity in bacteria
    • Zhu,L., Wang,Q., Tang,P., Araki,H. and Tian,D. (2009) Genomewide association between insertions/deletions and the nucleotide diversity in bacteria. Mol. Biol. Evol., 26, 2353-2361.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 2353-2361
    • Zhu, L.1    Wang, Q.2    Tang, P.3    Araki, H.4    Tian, D.5
  • 25
  • 26
    • 34547809931 scopus 로고    scopus 로고
    • Quantifying the impact of protein tertiary structure on molecular evolution
    • DOI 10.1093/molbev/msm097
    • Choi,S.C., Hobolth,A., Robinson,D.M., Kishino,H. and Thorne,J.L. (2007) Quantifying the impact of protein tertiary structure on molecular evolution. Mol. Biol. Evol., 24, 1769-1782. (Pubitemid 47236697)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1769-1782
    • Choi, S.C.1    Hobolth, A.2    Robinson, D.M.3    Kishino, H.4    Thorne, J.L.5
  • 27
    • 78650491535 scopus 로고    scopus 로고
    • Impact of indels on the flanking regions in structural domains
    • Zhang,Z., Huang,J., Wang,Z., Wang,L. and Gao,P. (2011) Impact of indels on the flanking regions in structural domains. Mol. Biol. Evol., 28, 291-301.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 291-301
    • Zhang, Z.1    Huang, J.2    Wang, Z.3    Wang, L.4    Gao, P.5
  • 30
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • DOI 10.1107/S0907444904026460
    • Krissinel,E. and Henrick,K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta. Crystallogr. D Biol. Crystallogr., 60, 2256-2268. (Pubitemid 41742778)
    • (2004) Acta Crystallographica Section D: Biological Crystallography , vol.60 , Issue.12 I , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 31
    • 13444279981 scopus 로고    scopus 로고
    • Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
    • DOI 10.1016/j.jmb.2004.12.032
    • Kolodny,R., Koehl,P. and Levitt,M. (2005) Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J. Mol. Biol., 346, 1173-1188. (Pubitemid 40215537)
    • (2005) Journal of Molecular Biology , vol.346 , Issue.4 , pp. 1173-1188
    • Kolodny, R.1    Koehl, P.2    Levitt, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.