메뉴 건너뛰기




Volumn 3, Issue , 2013, Pages

Protein structure alignment beyond spatial proximity

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84875164107     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep01448     Document Type: Article
Times cited : (145)

References (51)
  • 1
    • 66549119395 scopus 로고    scopus 로고
    • Advances and pitfalls of protein structural alignment
    • Hasegawa, H. & Holm, L. Advances and pitfalls of protein structural alignment. Current opinion in structural biology 19, 341-348 (2009).
    • (2009) Current Opinion in Structural Biology , vol.19 , pp. 341-348
    • Hasegawa, H.1    Holm, L.2
  • 2
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology 233, 123-123 (1993).
    • (1993) Journal of Molecular Biology , vol.233 , pp. 123-123
    • Holm, L.1    Sander, C.2
  • 3
    • 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. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica Section D: Biological Crystallography 60, 2256-2268 (2004). (Pubitemid 41742778)
    • (2004) Acta Crystallographica Section D: Biological Crystallography , vol.60 , Issue.12 I , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 4
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov, I. N. & Bourne, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein engineering 11, 739 (1998).
    • (1998) Protein Engineering , vol.11 , pp. 739
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 5
    • 0024349252 scopus 로고
    • Protein structure alignment
    • DOI 10.1016/0022-2836(89)90084-3
    • Taylor, W. R. & Orengo, C. A. Protein structure alignment. Journal of Molecular Biology 208, 1-22 (1989). (Pubitemid 19191513)
    • (1989) Journal of Molecular Biology , vol.208 , Issue.1 , pp. 1-22
    • Taylor, W.R.1    Orengo, C.A.2
  • 6
    • 44049099330 scopus 로고    scopus 로고
    • CLePAPS fast pair alignment of protein structures based on conformational letters
    • Wang, S. & Zheng, W. CLePAPS: fast pair alignment of protein structures based on conformational letters. Journal of bioinformatics and computational biology 6, 347 (2008).
    • (2008) Journal of Bioinformatics and Computational Biology , vol.6 , pp. 347
    • Wang, S.1    Zheng, W.2
  • 7
    • 3242887315 scopus 로고    scopus 로고
    • FATCAT a web server for flexible structure comparison and structure similarity searching
    • Ye, Y. & Godzik, A. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic acids research 32, W582 (2004).
    • (2004) Nucleic Acids Research , vol.32
    • Ye, Y.1    Godzik, A.2
  • 8
    • 12944271968 scopus 로고    scopus 로고
    • FAST: A novel protein structure alignment algorithm
    • DOI 10.1002/prot.20331
    • Zhu, J. & Weng, Z. FAST: a novel protein structure alignment algorithm. Proteins: Structure, Function, and Bioinformatics 58, 618-627 (2005). (Pubitemid 40176034)
    • (2005) Proteins: Structure, Function and Genetics , vol.58 , Issue.3 , pp. 618-627
    • Zhu, J.1    Weng, Z.2
  • 9
    • 0033833116 scopus 로고    scopus 로고
    • Protein structure alignment using environmental profiles
    • Jung, J. & Lee, B. Protein structure alignment using environmental profiles. Protein Engineering 13, 535-543 (2000).
    • (2000) Protein Engineering , vol.13 , pp. 535-543
    • Jung, J.1    Lee, B.2
  • 10
    • 0003301367 scopus 로고    scopus 로고
    • The VAST protein structure comparison method
    • Gibrat, J., Madej, T., Spouge, J. & Bryant, S. The VAST protein structure comparison method. Biophys J 72, 298 (1997).
    • (1997) Biophys J , vol.72 , pp. 298
    • Gibrat, J.1    Madej, T.2    Spouge, J.3    Bryant, S.4
  • 13
    • 25144458667 scopus 로고    scopus 로고
    • A new progressive-iterative algorithm for multiple structure alignment
    • Lupyan, D., Leo-Macias, A. & Ortiz, A. R. A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics 21, 3255 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 3255
    • Lupyan, D.1    Leo-Macias, A.2    Ortiz, A.R.3
  • 14
    • 38949150854 scopus 로고    scopus 로고
    • Local flexibility aids protein multiple structure alignment
    • Menke, M., Berger, B. & Cowen, L. Matt: local flexibility aids protein multiple structure alignment. PLoS computational biology 4, e10 (2008).
    • (2008) PLoS Computational Biology , vol.4
    • Menke, M.1    Berger, B.2    Matt, C.L.3
  • 15
    • 80052693672 scopus 로고    scopus 로고
    • Alignment of distantly related protein structures: Algorithm, bound and implications to homology modeling
    • Wang, S., Peng, J. & Xu, J. Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. Bioinformatics 27, 2537-2545 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2537-2545
    • Wang, S.1    Peng, J.2    Xu, J.3
  • 16
    • 80052720106 scopus 로고    scopus 로고
    • Fast multiple alignment of protein structures using conformational letter blocks
    • Wang, S. & Zheng, W. M. Fast Multiple Alignment of Protein Structures Using Conformational Letter Blocks. Open Bioinformatics Journal 3, 69-83 (2009).
    • (2009) Open Bioinformatics Journal , vol.3 , pp. 69-83
    • Wang, S.1    Zheng, W.M.2
  • 17
    • 19544388989 scopus 로고    scopus 로고
    • Multiple flexible structure alignment using partial order graphs
    • Ye, Y. & Godzik, A. Multiple flexible structure alignment using partial order graphs. Bioinformatics 21, 2362 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 2362
    • Ye, Y.1    Godzik, A.2
  • 18
    • 34548304928 scopus 로고    scopus 로고
    • Comparative analysis of protein structure alignments
    • Mayr, G., Domingues, F. & Lackner, P. Comparative analysis of protein structure alignments. BMC Structural Biology 7, 50 (2007).
    • (2007) BMC Structural Biology , vol.7 , pp. 50
    • Mayr, G.1    Domingues, F.2    Lackner, P.3
  • 19
    • 17644392830 scopus 로고    scopus 로고
    • TM-align a protein structure alignment algorithm based on the TM-score
    • Zhang, Y. & Skolnick, J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic acids research 33, 2302 (2005).
    • (2005) Nucleic Acids Research , vol.33 , pp. 2302
    • Zhang, Y.1    Skolnick, J.2
  • 20
    • 35448992938 scopus 로고    scopus 로고
    • Accuracy of structure-based sequence alignment of automatic methods
    • Kim, C. & Lee, B. Accuracy of structure-based sequence alignment of automatic methods. BMC bioinformatics 8, 355 (2007).
    • (2007) BMC Bioinformatics , vol.8 , pp. 355
    • Kim, C.1    Lee, B.2
  • 21
    • 84866980473 scopus 로고    scopus 로고
    • Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment
    • Nadimpalli, S., Daniels, N. & Cowen, L. Formatt: Formatt: Correcting Protein Multiple Structural Alignments by Incorporating Sequence Alignment. BMC Bioinformatics 13, 259 (2012).
    • (2012) BMC Bioinformatics , vol.13 , pp. 259
    • Nadimpalli, S.1    Daniels, N.2    Formatt, C.L.3
  • 23
    • 42449090264 scopus 로고    scopus 로고
    • PROMALS3D: A tool for multiple protein sequence and structure alignments
    • Pei, J., Kim, B. H. & Grishin, N. V. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic acids research 36, 2295 (2008).
    • (2008) Nucleic Acids Research , vol.36 , pp. 2295
    • Pei, J.1    Kim, B.H.2    Grishin, N.V.3
  • 24
    • 2942619012 scopus 로고    scopus 로고
    • 3DCoffee: Combining protein sequences and structures within multiple sequence alignments
    • DOI 10.1016/j.jmb.2004.04.058, PII S0022283604005212
    • O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D. G. & Notredame, C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. Journal of molecular biology 340, 385-395 (2004). (Pubitemid 38759917)
    • (2004) Journal of Molecular Biology , vol.340 , Issue.2 , pp. 385-395
    • O'Sullivan, O.1    Suhre, K.2    Abergel, C.3    Higgins, D.G.4    Notredame, C.5
  • 25
    • 49949086495 scopus 로고    scopus 로고
    • The use of a conformational alphabet for fast alignment of protein structures
    • Zheng, W. M. The use of a conformational alphabet for fast alignment of protein structures. Bioinformatics Research and Applications, 331-342 (2008).
    • (2008) Bioinformatics Research and Applications , pp. 331-342
    • Zheng, W.M.1
  • 27
    • 16344394781 scopus 로고    scopus 로고
    • SABmark-A benchmark for sequence alignment that covers the entire known fold space
    • Van Walle, I., Lasters, I. & Wyns, L. SABmark-a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 21, 1267 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 1267
    • Van Walle, I.1    Lasters, I.2    Wyns, L.3
  • 28
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • DOI 10.1002/prot.20264
    • Zhang, Y. & Skolnick, J. Scoring function for automated assessment of protein structure template quality. Proteins: Structure, Function, and Bioinformatics 57, 702-710 (2004). (Pubitemid 39626992)
    • (2004) Proteins: Structure, Function and Genetics , vol.57 , Issue.4 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 29
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • DOI 10.1093/nar/gkg571
    • Zemla, A. LGA: amethod for finding 3D similarities in protein structures. Nucleic acids research 31, 3370-3374 (2003). (Pubitemid 37442162)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3370-3374
    • Zemla, A.1
  • 30
    • 0032568649 scopus 로고    scopus 로고
    • A unified statistical framework for sequence comparison and structure comparison
    • Levitt, M. &Gerstein,M.A unified statistical framework for sequence comparison and structure comparison. Proceedings of the National Academy of sciences 95, 5913 (1998).
    • (1998) Proceedings of the National Academy of Sciences , vol.95 , pp. 5913
    • Levitt, M.1    Gerstein, M.2
  • 31
    • 13444262384 scopus 로고    scopus 로고
    • CDD: A Conserved Domain Database for protein classification
    • Marchler-Bauer, A. et al. CDD: a Conserved Domain Database for protein classification. Nucleic acids research 33, D192 (2005).
    • (2005) Nucleic Acids Research , vol.33
    • Marchler-Bauer, A.1
  • 32
    • 39749153446 scopus 로고    scopus 로고
    • MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs
    • DOI 10.1002/prot.21783
    • Cheng, H., Kim, B. H. & Grishin, N. V. MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs. Proteins: Structure, Function, and Bioinformatics 70, 1162-1166 (2008). (Pubitemid 351304076)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.4 , pp. 1162-1166
    • Cheng, H.1    Kim, B.-H.2    Grishin, N.V.3
  • 33
    • 38549170925 scopus 로고    scopus 로고
    • MALISAM: A database of structurally analogous motifs in proteins
    • Cheng, H., Kim, B. H. & Grishin, N. V. MALISAM: a database of structurally analogous motifs in proteins. Nucleic acids research 36, D211 (2008).
    • (2008) Nucleic Acids Research , vol.36
    • Cheng, H.1    Kim, B.H.2    Grishin, N.V.3
  • 34
    • 67949111155 scopus 로고    scopus 로고
    • Iterative refinement of structure-based sequence alignments by Seed Extension
    • Kim, C., Tai, C. H. & Lee, B. Iterative refinement of structure-based sequence alignments by Seed Extension. BMC bioinformatics 10, 210 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 210
    • Kim, C.1    Tai, C.H.2    Lee, B.3
  • 35
    • 3242880478 scopus 로고    scopus 로고
    • Fold Miner and LOCK 2: Protein structure comparison and motif discovery on the web
    • Shapiro, J. & Brutlag, D. FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web. Nucleic acids research 32, W536 (2004).
    • (2004) Nucleic Acids Research , vol.32
    • Shapiro, J.1    Brutlag, D.2
  • 36
    • 0041620359 scopus 로고    scopus 로고
    • MATRAS a program for protein 3D structure comparison
    • Kawabata, T. MATRAS: a program for protein 3D structure comparison. Nucleic acids research 31, 3367 (2003).
    • (2003) Nucleic Acids Research , vol.31 , pp. 3367
    • Kawabata, T.1
  • 37
    • 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. & Chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of molecular biology 247, 536-540 (1995).
    • (1995) Journal of Molecular Biology , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 38
    • 40849133659 scopus 로고    scopus 로고
    • Discrimination between distant homologs and structural analogs: Lessons from manually constructed, reliable data sets
    • Cheng, H., Kim, B. H. & Grishin, N. V. Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. Journal of molecular biology 377, 1265-1278 (2008).
    • (2008) Journal of Molecular Biology , vol.377 , pp. 1265-1278
    • Cheng, H.1    Kim, B.H.2    Grishin, N.V.3
  • 39
    • 20444484434 scopus 로고    scopus 로고
    • A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
    • DOI 10.1016/j.sbi.2005.05.011, PII S0959440X05000953
    • Moult, J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Current opinion in structural biology 15, 285-289 (2005). (Pubitemid 40826447)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.3 SPEC. ISSUE , pp. 285-289
    • Moult, J.1
  • 40
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • DOI 10.1093/nar/gki408
    • Söding, J., Biegert, A. & Lupas, A. N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic acids research 33, W244-W248 (2005). (Pubitemid 44529917)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISSUE
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 41
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25, 3389 (1997).
    • (1997) Nucleic Acids Research , vol.25 , pp. 3389
    • Altschul, S.F.1
  • 42
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 951
    • Söding, J.1
  • 43
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    • Xie, L. & Bourne, P. E. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proceedings of the National Academy of sciences 105, 5441 (2008).
    • (2008) Proceedings of the National Academy of Sciences , vol.105 , pp. 5441
    • Xie, L.1    Bourne, P.E.2
  • 44
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligandbinding site prediction and functional annotation
    • Brylinski, M. & Skolnick, J. A threading-based method (FINDSITE) for ligandbinding site prediction and functional annotation. Proceedings of the National Academy of sciences 105, 129 (2008).
    • (2008) Proceedings of the National Academy of Sciences , vol.105 , pp. 129
    • Brylinski, M.1    Skolnick, J.2
  • 45
    • 77956502131 scopus 로고    scopus 로고
    • IAlign: A method for the structural comparison of protein-protein interfaces
    • Gao, M. & Skolnick, J. iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics 26, 2259 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 2259
    • Gao, M.1    Skolnick, J.2
  • 48
    • 0027991446 scopus 로고
    • The FSSP database of structurally aligned protein fold families
    • Holm, L. & Sander, C. The FSSP database of structurally aligned protein fold families. Nucleic acids research 22, 3600 (1994).
    • (1994) Nucleic Acids Research , vol.22 , pp. 3600
    • Holm, L.1    Sander, C.2
  • 49
    • 77951961719 scopus 로고    scopus 로고
    • How significant is a protein structure similarity with TMscore5 0.5?
    • Xu, J. & Zhang, Y. How significant is a protein structure similarity with TMscore5 0.5? Bioinformatics 26, 889-895 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 889-895
    • Xu, J.1    Zhang, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.