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Volumn 34, Issue 12, 2018, Pages 2155-2157

Ssbio: A Python framework for structural systems biology

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; BIOLOGY; PROCEDURES; PROTEIN CONFORMATION; SOFTWARE;

EID: 85047568107     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bty077     Document Type: Article
Times cited : (26)

References (30)
  • 1
    • 34347380096 scopus 로고    scopus 로고
    • Structures in systems biology
    • Beltrao, P. et al. (2007) Structures in systems biology. Curr. Opin. Struct. Biol., 17, 378-384.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 378-384
    • Beltrao, P.1
  • 2
    • 77957803889 scopus 로고    scopus 로고
    • OpenStructure: A flexible software framework for computational structural biology
    • Biasini, M. et al. (2010) OpenStructure: a flexible software framework for computational structural biology. Bioinformatics, 26, 2626-2628.
    • (2010) Bioinformatics , vol.26 , pp. 2626-2628
    • Biasini, M.1
  • 3
    • 84976481496 scopus 로고    scopus 로고
    • Comparative genome-scale modelling of staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity
    • Bosi, E. et al. (2016). Comparative genome-scale modelling of staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. Proc. Natl. Acad. Sci. USA, 113(26), E3801-9.
    • (2016) Proc. Natl. Acad. Sci. USA , vol.113 , Issue.26 , pp. E3801-E3809
    • Bosi, E.1
  • 4
    • 85006401140 scopus 로고    scopus 로고
    • Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis
    • Broddrick, J.T. et al. (2016) Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. Proc. Natl. Acad. Sci. USA, 113, E8344-E8353.
    • (2016) Proc. Natl. Acad. Sci. USA , vol.113 , pp. E8344-E8353
    • Broddrick, J.T.1
  • 5
    • 84960384531 scopus 로고    scopus 로고
    • Systems biology of the structural proteome
    • Brunk, E. et al. (2016) Systems biology of the structural proteome. BMC Syst. Biol., 10, 26.
    • (2016) BMC Syst. Biol. , vol.10 , pp. 26
    • Brunk, E.1
  • 6
    • 78049445175 scopus 로고    scopus 로고
    • Drug off-target effects predicted using structural analysis in the context of a metabolic network model
    • Chang, R.L. et al. (2010) Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput. Biol., 6, e1000938.
    • (2010) PLoS Comput. Biol. , vol.6 , pp. e1000938
    • Chang, R.L.1
  • 7
    • 84878756325 scopus 로고    scopus 로고
    • Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli
    • Chang, R.L. et al. (2013). Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science, 340(6137), 1220-1223.
    • (2013) Science , vol.340 , Issue.6137 , pp. 1220-1223
    • Chang, R.L.1
  • 8
    • 85032175673 scopus 로고    scopus 로고
    • Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation
    • Chen, K. et al. (2017) Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proc. Natl. Acad. Sci. USA, 114, 11548-11553.
    • (2017) Proc. Natl. Acad. Sci. USA , vol.114 , pp. 11548-11553
    • Chen, K.1
  • 9
    • 23144465987 scopus 로고    scopus 로고
    • SCRATCH: A protein structure and structural feature prediction server
    • Cheng, J. et al. (2005) SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res, 33 (Web Server issue), W72-W76.
    • (2005) Nucleic Acids Res , vol.33 , Issue.WEB SERVER ISS , pp. W72-W76
    • Cheng, J.1
  • 10
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: Freely available python tools for computational molecular biology and bioinformatics
    • Cock, P.J.A. et al. (2009) Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423.
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Cock, P.J.A.1
  • 11
    • 84881152495 scopus 로고    scopus 로고
    • COBRApy: Constraints-based reconstruction and analysis for python
    • Ebrahim, A. et al. (2013) COBRApy: constraints-based reconstruction and analysis for python. BMC Syst. Biol., 7, 74.
    • (2013) BMC Syst. Biol. , vol.7 , pp. 74
    • Ebrahim, A.1
  • 12
    • 81355123249 scopus 로고    scopus 로고
    • Software for systems biology: From tools to integrated platforms
    • Ghosh, S. et al. (2011) Software for systems biology: from tools to integrated platforms. Nat. Rev. Genet., 12, 821-832.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 821-832
    • Ghosh, S.1
  • 13
    • 34147192127 scopus 로고    scopus 로고
    • Biskit-A software platform for structural bioinformatics
    • Grunberg, R. et al. (2007) Biskit-A software platform for structural bioinformatics. Bioinformatics, 23, 769-770.
    • (2007) Bioinformatics , vol.23 , pp. 769-770
    • Grunberg, R.1
  • 15
    • 0344033635 scopus 로고    scopus 로고
    • PDB file parser and structure class implemented in python
    • Hamelryck, T. and Manderick, B. (2003) PDB file parser and structure class implemented in python. Bioinformatics, 19, 2308-2310.
    • (2003) Bioinformatics , vol.19 , pp. 2308-2310
    • Hamelryck, T.1    Manderick, B.2
  • 16
    • 0020997912 scopus 로고
    • DSSP: Definition of secondary structure of proteins given a set of 3D coordinates
    • Kabsch, W. and Sander, C. (1983) DSSP: definition of secondary structure of proteins given a set of 3D coordinates. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 17
    • 84940751701 scopus 로고    scopus 로고
    • Escher: A web application for building, sharing, and embedding Data-Rich visualizations of biological pathways
    • King, Z.A. et al. (2015) Escher: a web application for building, sharing, and embedding Data-Rich visualizations of biological pathways. PLoS Comput. Biol., 11, e1004321.
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1004321
    • King, Z.A.1
  • 19
    • 84980047670 scopus 로고    scopus 로고
    • A multi-scale computational platform to mechanistically assess the effect of genetic variation on drug responses in human erythrocyte metabolism
    • Mih, N. et al. (2016) A multi-scale computational platform to mechanistically assess the effect of genetic variation on drug responses in human erythrocyte metabolism. PLoS Comput. Biol., 12, e1005039.
    • (2016) PLoS Comput. Biol. , vol.12 , pp. e1005039
    • Mih, N.1
  • 20
    • 84908636701 scopus 로고    scopus 로고
    • Covering complete proteomes with x-ray structures: A current snapshot Acta Crystallogr
    • Mizianty, M.J. et al. (2014) Covering complete proteomes with x-ray structures: a current snapshot. Acta Crystallogr. D Biol. Crystallogr., 70, 2781-2793.
    • (2014) D Biol. Crystallogr. , vol.70 , pp. 2781-2793
    • Mizianty, M.J.1
  • 21
    • 84991740197 scopus 로고    scopus 로고
    • Multi-omics quantification of species variation of Escherichia coli links molecular features with strain phenotypes
    • Monk, J.M. et al. (2016) Multi-omics quantification of species variation of Escherichia coli links molecular features with strain phenotypes. Cell Syst., 3, 238-251.e12.
    • (2016) Cell Syst. , vol.3 , pp. 238e12-251e12
    • Monk, J.M.1
  • 22
    • 85031310018 scopus 로고    scopus 로고
    • IML1515, a knowledgebase that computes Escherichia coli traits
    • Monk, J.M. et al. (2017) iML1515, a knowledgebase that computes Escherichia coli traits. Nat. Biotechnol., 35, 904-908.
    • (2017) Nat. Biotechnol. , vol.35 , pp. 904-908
    • Monk, J.M.1
  • 23
    • 85045855391 scopus 로고    scopus 로고
    • NGLview: Interactive molecular graphics for jupyter notebooks
    • Nguyen, H. et al. (2017). NGLview: interactive molecular graphics for jupyter notebooks. Bioinformatics, 34, 1241-1242.
    • (2017) Bioinformatics , vol.34 , pp. 1241-1242
    • Nguyen, H.1
  • 24
    • 84930227327 scopus 로고    scopus 로고
    • Using genome-scale models to predict biological capabilities
    • O'Brien, E.J. et al. (2015). Using genome-scale models to predict biological capabilities. Cell, 161(5), 971-987.
    • (2015) Cell , vol.161 , Issue.5 , pp. 971-987
    • O'Brien, E.J.1
  • 25
    • 84963941048 scopus 로고    scopus 로고
    • Aquaria: Simplifying discovery and insight from protein structures
    • O'Donoghue, S.I. et al. (2015). Aquaria: simplifying discovery and insight from protein structures. Nat. Methods, 12(2), 98-99.
    • (2015) Nat. Methods , vol.12 , Issue.2 , pp. 98-99
    • O'Donoghue, S.I.1
  • 26
    • 84899131429 scopus 로고    scopus 로고
    • Comparisons of shewanella strains based on genome annotations, modeling, and experiments
    • Ong, W.K. et al. (2014) Comparisons of shewanella strains based on genome annotations, modeling, and experiments. BMC Syst. Biol., 8, 31.
    • (2014) BMC Syst. Biol. , vol.8 , pp. 31
    • Ong, W.K.1
  • 27
    • 84979865146 scopus 로고    scopus 로고
    • NGL viewer: A web application for molecular visualization
    • Rose, A.S. and Hildebrand, P.W. (2015) NGL viewer: a web application for molecular visualization. Nucleic Acids Res., 43, W576-W579.
    • (2015) Nucleic Acids Res. , vol.43 , pp. W576-W579
    • Rose, A.S.1    Hildebrand, P.W.2
  • 28
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: A unified platform for automated protein structure and function prediction
    • Roy, A. et al. (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc., 5, 725-738.
    • (2010) Nat. Protoc. , vol.5 , pp. 725-738
    • Roy, A.1
  • 29
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner, M.F. et al. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38, 305-320.
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1
  • 30
    • 70349345898 scopus 로고    scopus 로고
    • Three-dimensional structural view of the central metabolic network of thermotoga maritima
    • Zhang, Y. et al. (2009). Three-dimensional structural view of the central metabolic network of thermotoga maritima. Science, 325(5947), 1544-1549.
    • (2009) Science , vol.325 , Issue.5947 , pp. 1544-1549
    • Zhang, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.