메뉴 건너뛰기




Volumn 116, Issue 32, 2019, Pages 15930-15938

Assembling multidomain protein structures through analogous global structural alignments

Author keywords

Domain assembly; Multidomain protein; Multidomain template recognition; Protein structure prediction

Indexed keywords

CASPASE 12; CASPASE 13; CROSS LINKING REAGENT; PROTEIN;

EID: 85070206977     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1905068116     Document Type: Article
Times cited : (80)

References (29)
  • 1
    • 0021814798 scopus 로고
    • Comparison of the independent solvent structures of dimeric alpha-chymotrypsin with themselves and with gamma-chymotrypsin
    • R. A. Blevins, A. Tulinsky, Comparison of the independent solvent structures of dimeric alpha-chymotrypsin with themselves and with gamma-chymotrypsin. J. Biol. Chem. 260, 8865–8872 (1985).
    • (1985) J. Biol. Chem. , vol.260 , pp. 8865-8872
    • Blevins, R.A.1    Tulinsky, A.2
  • 3
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: A unified platform for automated protein structure and function prediction
    • A. Roy, A. Kucukural, Y. Zhang, I-TASSER: A unified platform for automated protein structure and function prediction. Nat. Protoc. 5, 725–738 (2010).
    • (2010) Nat. Protoc. , vol.5 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 4
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Y. Zhang, I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9, 40 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 40
    • Zhang, Y.1
  • 5
    • 84925156346 scopus 로고    scopus 로고
    • The I-TASSER suite: Protein structure and function prediction
    • J. Yang et al., The I-TASSER suite: Protein structure and function prediction. Nat. Methods 12, 7–8 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 7-8
    • Yang, J.1
  • 6
    • 84862225232 scopus 로고    scopus 로고
    • Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
    • D. Xu, Y. Zhang, Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 80, 1715–1735 (2012).
    • (2012) Proteins , vol.80 , pp. 1715-1735
    • Xu, D.1    Zhang, Y.2
  • 7
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with rosetta
    • R. Das, D. Baker, Macromolecular modeling with rosetta. Annu. Rev. Biochem. 77, 363–382 (2008).
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 8
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • P. Bradley, K. M. Misura, D. Baker, Toward high-resolution de novo structure prediction for small proteins. Science 309, 1868–1871 (2005).
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.2    Baker, D.3
  • 9
    • 84936763474 scopus 로고    scopus 로고
    • AIDA: Ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction
    • D. Xu, L. Jaroszewski, Z. Li, A. Godzik, AIDA: Ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. Bioinformatics 31, 2098–2105 (2015).
    • (2015) Bioinformatics , vol.31 , pp. 2098-2105
    • Xu, D.1    Jaroszewski, L.2    Li, Z.3    Godzik, A.4
  • 10
    • 33846471085 scopus 로고    scopus 로고
    • Prediction of structures of multidomain proteins from structures of the individual domains
    • A. M. Wollacott, A. Zanghellini, P. Murphy, D. Baker, Prediction of structures of multidomain proteins from structures of the individual domains. Protein Sci. 16, 165–175 (2007).
    • (2007) Protein Sci , vol.16 , pp. 165-175
    • Wollacott, A.M.1    Zanghellini, A.2    Murphy, P.3    Baker, D.4
  • 11
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Y. Zhang, J. Skolnick, TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 33, 2302–2309 (2005).
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 13
    • 0034491038 scopus 로고    scopus 로고
    • Protein domain decomposition using a graph-theoretic approach
    • Correction in: Bioinformatics 17, 290 2001
    • Y. Xu, D. Xu, H. N. Gabow, Protein domain decomposition using a graph-theoretic approach. Bioinformatics 16, 1091–1104 (2000). Correction in: Bioinformatics 17, 290 (2001).
    • (2000) Bioinformatics , vol.16 , pp. 1091-1104
    • Xu, Y.1    Xu, D.2    Gabow, H.N.3
  • 14
    • 84976904331 scopus 로고    scopus 로고
    • Gene3D: Expanding the utility of domain assignments
    • S. D. Lam et al., Gene3D: Expanding the utility of domain assignments. Nucleic Acids Res. 44, D404–D409 (2016).
    • (2016) Nucleic Acids Res , vol.44 , pp. D404-D409
    • Lam, S.D.1
  • 15
    • 85007574062 scopus 로고    scopus 로고
    • SCOPE: Manual curation and artifact removal in the structural classification of proteins—Extended database
    • J.-M. Chandonia, N. K. Fox, S. E. Brenner, SCOPe: Manual curation and artifact removal in the structural classification of proteins—Extended database. J. Mol. Biol. 429, 348–355 (2017).
    • (2017) J. Mol. Biol. , vol.429 , pp. 348-355
    • Chandonia, J.-M.1    Fox, N.K.2    Brenner, S.E.3
  • 16
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure template quality. Proteins 57, 702–710 (2004).
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 17
    • 38049034590 scopus 로고    scopus 로고
    • Comparative protein structure modeling using MODELLER
    • B. Webb, A. Sali, Comparative protein structure modeling using MODELLER. Curr. Protoc. Bioinformatics 47, 1–32 (2014).
    • (2014) Curr. Protoc. Bioinformatics , vol.47 , pp. 1-32
    • Webb, B.1    Sali, A.2
  • 18
    • 44949145113 scopus 로고    scopus 로고
    • Progress and challenges in protein structure prediction
    • Y. Zhang, Progress and challenges in protein structure prediction. Curr. Opin. Struct. Biol. 18, 342–348 (2008).
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 342-348
    • Zhang, Y.1
  • 19
    • 85037375235 scopus 로고    scopus 로고
    • Evaluation of the template-based modeling in CASP12
    • A. Kryshtafovych et al., Evaluation of the template-based modeling in CASP12. Proteins 86 (suppl. 1), 321–334 (2018).
    • (2018) Proteins , vol.86 , pp. 321-334
    • Kryshtafovych, A.1
  • 20
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • J. Söding, Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951–960 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Söding, J.1
  • 21
    • 34250851687 scopus 로고    scopus 로고
    • Lomets: A local meta-threading-server for protein structure prediction
    • S. Wu, Y. Zhang, LOMETS: A local meta-threading-server for protein structure prediction. Nucleic Acids Res. 35, 3375–3382 (2007).
    • (2007) Nucleic Acids Res , vol.35 , pp. 3375-3382
    • Wu, S.1    Zhang, Y.2
  • 22
    • 85033794178 scopus 로고    scopus 로고
    • Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12
    • C. Zhang, S. M. Mortuza, B. He, Y. Wang, Y. Zhang, Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins 86 (suppl. 1), 136–151 (2018).
    • (2018) Proteins , vol.86 , pp. 136-151
    • Zhang, C.1    Mortuza, S.M.2    He, B.3    Wang, Y.4    Zhang, Y.5
  • 23
    • 85030635867 scopus 로고    scopus 로고
    • Protein structure prediction using Rosetta in CASP12
    • S. Ovchinnikov, H. Park, D. E. Kim, F. DiMaio, D. Baker, Protein structure prediction using Rosetta in CASP12. Proteins 86 (suppl. 1), 113–121 (2018).
    • (2018) Proteins , vol.86 , pp. 113-121
    • Ovchinnikov, S.1    Park, H.2    Kim, D.E.3    DiMaio, F.4    Baker, D.5
  • 24
    • 84856497340 scopus 로고    scopus 로고
    • Putting the pieces together: Integrative modeling platform software for structure determination of macromolecular assemblies
    • D. Russel et al., Putting the pieces together: Integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol. 10, e1001244 (2012).
    • (2012) PLoS Biol , vol.10
    • Russel, D.1
  • 26
    • 35949020425 scopus 로고
    • Replica Monte Carlo simulation of spin glasses
    • R. H. Swendsen, J.-S. Wang, Replica Monte Carlo simulation of spin glasses. Phys. Rev. Lett. 57, 2607–2609 (1986).
    • (1986) Phys. Rev. Lett. , vol.57 , pp. 2607-2609
    • Swendsen, R.H.1    Wang, J.-S.2
  • 27
    • 0041843696 scopus 로고    scopus 로고
    • Touchstone II: A new approach to ab initio protein structure prediction
    • Y. Zhang, A. Kolinski, J. Skolnick, TOUCHSTONE II: A new approach to ab initio protein structure prediction. Biophys. J. 85, 1145–1164 (2003).
    • (2003) Biophys. J. , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 29
    • 82955239912 scopus 로고    scopus 로고
    • Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling
    • J. Zhang, Y. Liang, Y. Zhang, Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure 19, 1784–1795 (2011).
    • (2011) Structure , vol.19 , pp. 1784-1795
    • Zhang, J.1    Liang, Y.2    Zhang, Y.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.