메뉴 건너뛰기




Volumn 28, Issue 1, 2014, Pages 96-104

Uncertainty in integrative structural modeling

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTICAL ERROR; BAYES THEOREM; DATA ANALYSIS; DATA EXTRACTION; DATA SYNTHESIS; EXPERIMENTAL STUDY; INFORMATION MODEL; INFORMATION RETRIEVAL; INTEGRATIVE STRUCTURAL MODELING; PRIORITY JOURNAL; PROCESS OPTIMIZATION; REVIEW; SAMPLING; SCORING SYSTEM; SIMULATION; CLUSTER ANALYSIS; DATA COLLECTION METHOD; INFORMATION SYSTEM; MEASUREMENT ACCURACY; MEASUREMENT PRECISION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STANDARDIZATION; SYSTEMATIC ERROR; VALIDATION PROCESS; X RAY CRYSTALLOGRAPHY; CHEMICAL STRUCTURE; THEORETICAL MODEL;

EID: 84908116377     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2014.08.001     Document Type: Review
Times cited : (85)

References (66)
  • 1
    • 0026597444 scopus 로고
    • Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992, 355:472-475.
    • (1992) Nature , vol.355 , pp. 472-475
    • Brünger, A.T.1
  • 5
    • 84862222355 scopus 로고    scopus 로고
    • Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution
    • Jacques D.A., Guss J.M., Svergun D.I., Trewhella J. Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution. Acta Crystallogr D Biol Crystallogr 2012, 68:620-626.
    • (2012) Acta Crystallogr D Biol Crystallogr , vol.68 , pp. 620-626
    • Jacques, D.A.1    Guss, J.M.2    Svergun, D.I.3    Trewhella, J.4
  • 9
    • 0019987933 scopus 로고
    • The correlation averaging of a regularly arranged bacterial cell envelope protein
    • Saxton W.O., Baumeister W. The correlation averaging of a regularly arranged bacterial cell envelope protein. J Microsc 1982, 127:127-138.
    • (1982) J Microsc , vol.127 , pp. 127-138
    • Saxton, W.O.1    Baumeister, W.2
  • 10
    • 0000313739 scopus 로고
    • Exact filters for general geometry three dimensional reconstruction
    • Harauz G., van Heel M. Exact filters for general geometry three dimensional reconstruction. Proc IEEE Computer Vision Pattern Recogn 1986, 78:146-156.
    • (1986) Proc IEEE Computer Vision Pattern Recogn , vol.78 , pp. 146-156
    • Harauz, G.1    van Heel, M.2
  • 12
    • 84866078359 scopus 로고    scopus 로고
    • Prevention of overfitting in cryo-EM structure determination
    • Scheres S.H.W., Chen S. Prevention of overfitting in cryo-EM structure determination. Nat Methods 2012, 9:853-854.
    • (2012) Nat Methods , vol.9 , pp. 853-854
    • Scheres, S.H.W.1    Chen, S.2
  • 13
    • 84880607763 scopus 로고    scopus 로고
    • High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy
    • Chen S., McMullan G., Faruqi A.R., Murshudov G.N., Short J.M., Scheres S.H.W., Henderson R. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 2013, 135:24-35.
    • (2013) Ultramicroscopy , vol.135 , pp. 24-35
    • Chen, S.1    McMullan, G.2    Faruqi, A.R.3    Murshudov, G.N.4    Short, J.M.5    Scheres, S.H.W.6    Henderson, R.7
  • 14
    • 84894480986 scopus 로고    scopus 로고
    • ResLog plots as an empirical metric of the quality of cryo-EM reconstructions
    • Stagg S.M., Noble A.J., Spilman M., Chapman M.S. ResLog plots as an empirical metric of the quality of cryo-EM reconstructions. J Struct Biol 2014, 185:418-426.
    • (2014) J Struct Biol , vol.185 , pp. 418-426
    • Stagg, S.M.1    Noble, A.J.2    Spilman, M.3    Chapman, M.S.4
  • 15
    • 84876800465 scopus 로고    scopus 로고
    • Accurate assessment of mass, models and resolution by small-angle scattering
    • Rambo R.P., Tainer J.A. Accurate assessment of mass, models and resolution by small-angle scattering. Nature 2013, 496:477-481.
    • (2013) Nature , vol.496 , pp. 477-481
    • Rambo, R.P.1    Tainer, J.A.2
  • 16
    • 79958045453 scopus 로고    scopus 로고
    • Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law
    • Rambo R.P., Tainer J.A. Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers 2011, 95:559-571.
    • (2011) Biopolymers , vol.95 , pp. 559-571
    • Rambo, R.P.1    Tainer, J.A.2
  • 17
    • 84883481556 scopus 로고    scopus 로고
    • The Protein Model Portal-a comprehensive resource for protein structure and model information
    • bat031
    • Haas J., Roth S., Arnold K., Kiefer F., Schmidt T., Bordoli L., Schwede T. The Protein Model Portal-a comprehensive resource for protein structure and model information. Database (Oxford) 2013, 2013. bat031.
    • (2013) Database (Oxford) , vol.2013
    • Haas, J.1    Roth, S.2    Arnold, K.3    Kiefer, F.4    Schmidt, T.5    Bordoli, L.6    Schwede, T.7
  • 18
  • 19
    • 0037435031 scopus 로고    scopus 로고
    • From words to literature in structural proteomics
    • Sali A., Glaeser R., Earnest T., Baumeister W. From words to literature in structural proteomics. Nature 2003, 422:216-225.
    • (2003) Nature , vol.422 , pp. 216-225
    • Sali, A.1    Glaeser, R.2    Earnest, T.3    Baumeister, W.4
  • 22
    • 84874181173 scopus 로고    scopus 로고
    • Biochemistry integrative structural biology
    • Ward A.B., Sali A., Wilson I.A. Biochemistry integrative structural biology. Science 2013, 339:913-915.
    • (2013) Science , vol.339 , pp. 913-915
    • Ward, A.B.1    Sali, A.2    Wilson, I.A.3
  • 23
    • 79851510675 scopus 로고    scopus 로고
    • Statistical mechanics analysis of sparse data
    • Habeck M. Statistical mechanics analysis of sparse data. J Struct Biol 2011, 173:541-548.
    • (2011) J Struct Biol , vol.173 , pp. 541-548
    • Habeck, M.1
  • 24
    • 84877045691 scopus 로고    scopus 로고
    • Everything happens at once-deconvolving systematic effects in X-ray data processing
    • Borek D., Otwinowski Z. Everything happens at once-deconvolving systematic effects in X-ray data processing. Adv Methods Biomol Crystallogr 2013, 105-112.
    • (2013) Adv Methods Biomol Crystallogr , pp. 105-112
    • Borek, D.1    Otwinowski, Z.2
  • 25
    • 33845183709 scopus 로고
    • Automated stereospecific proton NMR assignments and their impact on the precision of protein structure determinations in solution
    • Guentert P., Braun W., Billeter M. Automated stereospecific proton NMR assignments and their impact on the precision of protein structure determinations in solution. J Am Chem Soc 1989, 111:3997-4004.
    • (1989) J Am Chem Soc , vol.111 , pp. 3997-4004
    • Guentert, P.1    Braun, W.2    Billeter, M.3
  • 28
    • 79960400833 scopus 로고    scopus 로고
    • Xwalk: computing and visualizing distances in cross-linking experiments
    • Kahraman A., Malmström L., Aebersold R. Xwalk: computing and visualizing distances in cross-linking experiments. Bioinformatics 2011, 27:2163-2164.
    • (2011) Bioinformatics , vol.27 , pp. 2163-2164
    • Kahraman, A.1    Malmström, L.2    Aebersold, R.3
  • 29
    • 84908221627 scopus 로고    scopus 로고
    • Modelling dynamics in protein crystal structures by ensemble refinement
    • Burnley B.T., Afonine P.V., Adams P.D., Gros P. Modelling dynamics in protein crystal structures by ensemble refinement. Elife 2012, 1:e00311.
    • (2012) Elife , vol.1
    • Burnley, B.T.1    Afonine, P.V.2    Adams, P.D.3    Gros, P.4
  • 31
    • 34247891557 scopus 로고    scopus 로고
    • Structural characterization of flexible proteins using small-angle X-ray scattering
    • Bernado P., Mylonas E., Petoukhov M.V., Blackledge M., Svergun D.I. Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc 2007, 129:5656-5664.
    • (2007) J Am Chem Soc , vol.129 , pp. 5656-5664
    • Bernado, P.1    Mylonas, E.2    Petoukhov, M.V.3    Blackledge, M.4    Svergun, D.I.5
  • 32
    • 67650992092 scopus 로고    scopus 로고
    • Structure and flexibility within proteins as identified through small angle X-ray scattering
    • Pelikan M., Hura G.L., Hammel M. Structure and flexibility within proteins as identified through small angle X-ray scattering. Gen Physiol Biophys 2009, 28:174-189.
    • (2009) Gen Physiol Biophys , vol.28 , pp. 174-189
    • Pelikan, M.1    Hura, G.L.2    Hammel, M.3
  • 33
    • 78650948314 scopus 로고    scopus 로고
    • SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions
    • Rózycki B., Kim Y.C., Hummer G. SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Struct/Folding Design 2011, 19:109-116.
    • (2011) Struct/Folding Design , vol.19 , pp. 109-116
    • Rózycki, B.1    Kim, Y.C.2    Hummer, G.3
  • 34
    • 84887782926 scopus 로고    scopus 로고
    • Recovering a representative conformational ensemble from underdetermined macromolecular structural data
    • Berlin K., Castañeda C.A., Schneidman-Duhovny D., Sali A., Nava-Tudela A., Fushman D. Recovering a representative conformational ensemble from underdetermined macromolecular structural data. J Am Chem Soc 2013, 135:16595-16609.
    • (2013) J Am Chem Soc , vol.135 , pp. 16595-16609
    • Berlin, K.1    Castañeda, C.A.2    Schneidman-Duhovny, D.3    Sali, A.4    Nava-Tudela, A.5    Fushman, D.6
  • 35
    • 77950517750 scopus 로고    scopus 로고
    • Automated multi-model reconstruction from single-particle electron microscopy data
    • Shatsky M., Hall R.J., Nogales E., Malik J., Brenner S.E. Automated multi-model reconstruction from single-particle electron microscopy data. J Struct Biol 2010, 170:98-108.
    • (2010) J Struct Biol , vol.170 , pp. 98-108
    • Shatsky, M.1    Hall, R.J.2    Nogales, E.3    Malik, J.4    Brenner, S.E.5
  • 36
    • 22144489530 scopus 로고    scopus 로고
    • Inferential structure determination
    • Rieping W., Habeck M., Nilges M. Inferential structure determination. Science 2005, 309:303-306.
    • (2005) Science , vol.309 , pp. 303-306
    • Rieping, W.1    Habeck, M.2    Nilges, M.3
  • 38
    • 84868444740 scopus 로고    scopus 로고
    • RELION: implementation of a Bayesian approach to cryo-EM structure determination
    • Scheres S.H.W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 2012, 180:519-530.
    • (2012) J Struct Biol , vol.180 , pp. 519-530
    • Scheres, S.H.W.1
  • 39
    • 84855818650 scopus 로고    scopus 로고
    • A Bayesian view on cryo-EM structure determination
    • Scheres S.H.W. A Bayesian view on cryo-EM structure determination. J Mol Biol 2012, 415:406-418.
    • (2012) J Mol Biol , vol.415 , pp. 406-418
    • Scheres, S.H.W.1
  • 40
    • 41949119820 scopus 로고    scopus 로고
    • ISD: a software package for Bayesian NMR structure calculation
    • Rieping W., Nilges M., Habeck M. ISD: a software package for Bayesian NMR structure calculation. Bioinformatics 2008, 24:1104-1105.
    • (2008) Bioinformatics , vol.24 , pp. 1104-1105
    • Rieping, W.1    Nilges, M.2    Habeck, M.3
  • 42
    • 84878580683 scopus 로고    scopus 로고
    • Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles
    • Bai X-C., Fernández I.S., McMullan G., Scheres S.H. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. Elife 2013, 2:e00461.
    • (2013) Elife , vol.2
    • Bai, X.-C.1    Fernández, I.S.2    McMullan, G.3    Scheres, S.H.4
  • 44
    • 84888042652 scopus 로고    scopus 로고
    • Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies
    • Cossio P., Hummer G. Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies. J Struct Biol 2013, 184:427-437.
    • (2013) J Struct Biol , vol.184 , pp. 427-437
    • Cossio, P.1    Hummer, G.2
  • 45
    • 84929417365 scopus 로고    scopus 로고
    • Cys-scanning Disulfide crosslinking and Bayesian modeling suggest scissoring motions in the histidine kinase, PhoQ
    • (in press), pii:S0969-2126(14)00204-4
    • Molnar K.S., Bonomi M., Pellarin R., Clinthorne G.D., Gonzalez G., Goldberg S.D., Sali A., DeGrado W.F. Cys-scanning Disulfide crosslinking and Bayesian modeling suggest scissoring motions in the histidine kinase, PhoQ. Structure 2014, 22. (in press), pii:S0969-2126(14)00204-4.
    • (2014) Structure , vol.22
    • Molnar, K.S.1    Bonomi, M.2    Pellarin, R.3    Clinthorne, G.D.4    Gonzalez, G.5    Goldberg, S.D.6    Sali, A.7    DeGrado, W.F.8
  • 46
  • 48
    • 84900348596 scopus 로고    scopus 로고
    • Optimized atomic statistical potentials: assessment of protein interfaces and loops
    • Dong G.Q., Fan H., Schneidman-Duhovny D., Webb B., Sali A. Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinformatics 2013, 29:3158-3166.
    • (2013) Bioinformatics , vol.29 , pp. 3158-3166
    • Dong, G.Q.1    Fan, H.2    Schneidman-Duhovny, D.3    Webb, B.4    Sali, A.5
  • 50
    • 0003242437 scopus 로고
    • The jackknife, the bootstrap and other resampling plans.
    • Efron B, Efron B. The jackknife, the bootstrap and other resampling plans. 1982. http://epubs.siam.org/doi/abs/10.1137/1.9781611970319.fm.
    • (1982)
    • Efron, B.1    Efron, B.2
  • 51
    • 84863540362 scopus 로고    scopus 로고
    • Physical tethering and volume exclusion determine higher-order genome organization in budding yeast
    • Tjong H., Gong K., Chen L., Alber F. Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. Genome Res 2012, 22:1295-1305.
    • (2012) Genome Res , vol.22 , pp. 1295-1305
    • Tjong, H.1    Gong, K.2    Chen, L.3    Alber, F.4
  • 55
    • 84857385799 scopus 로고    scopus 로고
    • Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling
    • Kalisman N., Adams C.M., Levitt M. Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling. Proc Natl Acad Sci U S A 2012, 109:2884-2889.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 2884-2889
    • Kalisman, N.1    Adams, C.M.2    Levitt, M.3
  • 62
    • 84900828258 scopus 로고    scopus 로고
    • Transient electrostatic interactions dominate the conformational equilibrium sampled by multi-domain splicing factor U2AF65: a combined NMR and SAXS study
    • Huang J-R., Warner L.R., Sanchez C., Gabel F., Madl T., Mackereth C.D., Sattler M., Blackledge M. Transient electrostatic interactions dominate the conformational equilibrium sampled by multi-domain splicing factor U2AF65: a combined NMR and SAXS study. J Am Chem Soc 2014, 10.1021/ja502030n.
    • (2014) J Am Chem Soc
    • Huang, J.-R.1    Warner, L.R.2    Sanchez, C.3    Gabel, F.4    Madl, T.5    Mackereth, C.D.6    Sattler, M.7    Blackledge, M.8
  • 65
    • 79952282038 scopus 로고    scopus 로고
    • Structure determination of genomic domains by satisfaction of spatial restraints
    • Baù D., Marti-Renom M.A. Structure determination of genomic domains by satisfaction of spatial restraints. Chromosome Res 2011, 19:25-35.
    • (2011) Chromosome Res , vol.19 , pp. 25-35
    • Baù, D.1    Marti-Renom, M.A.2
  • 66
    • 84862917808 scopus 로고    scopus 로고
    • Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
    • Kalhor R., Tjong H., Jayathilaka N., Alber F., Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol 2012, 30:90-98.
    • (2012) Nat Biotechnol , vol.30 , pp. 90-98
    • Kalhor, R.1    Tjong, H.2    Jayathilaka, N.3    Alber, F.4    Chen, L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.