메뉴 건너뛰기




Volumn 44, Issue 1, 2016, Pages W424-W429

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

Author keywords

[No Author keywords available]

Indexed keywords

DNA; INTERLEUKIN 1 RECEPTOR LIKE 1 PROTEIN; INTERLEUKIN 33; POLYNUCLEOTIDE 5' HYDROXYL KINASE; MULTIPROTEIN COMPLEX; PROTEIN;

EID: 85013011986     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw389     Document Type: Article
Times cited : (381)

References (37)
  • 4
    • 37149049312 scopus 로고    scopus 로고
    • X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution
    • Putnam,C.D., Hammel,M., Hura,G.L. and Tainer,J.A. (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q. Rev. Biophys., 40, 191–285.
    • (2007) Q. Rev. Biophys , vol.40 , pp. 191-285
    • Putnam, C.D.1    Hammel, M.2    Hura, G.L.3    Tainer, J.A.4
  • 5
    • 84877778935 scopus 로고    scopus 로고
    • Super-resolution in solution X-ray scattering and its applications to structural systems biology
    • Rambo,R.P. and Tainer,J.A. (2013) Super-resolution in solution X-ray scattering and its applications to structural systems biology. Annu. Rev. Biophys., 42, 415–441.
    • (2013) Annu. Rev. Biophys , vol.42 , pp. 415-441
    • Rambo, R.P.1    Tainer, J.A.2
  • 6
    • 0031807272 scopus 로고    scopus 로고
    • Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm
    • Chacon,P., Moran,F., Diaz,J.F., Pantos,E. and Andreu,J.M. (1998) Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys. J., 74, 2760–2775.
    • (1998) Biophys. J , vol.74 , pp. 2760-2775
    • Chacon, P.1    Moran, F.2    Diaz, J.F.3    Pantos, E.4    Andreu, J.M.5
  • 7
    • 0033001996 scopus 로고    scopus 로고
    • Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing
    • Svergun,D.I. (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J., 76, 2879–2886.
    • (1999) Biophys. J , vol.76 , pp. 2879-2886
    • Svergun, D.I.1
  • 8
    • 0035010533 scopus 로고    scopus 로고
    • Determination of domain structure of proteins from X-ray solution scattering
    • Svergun,D.I., Petoukhov,M.V. and Koch,M.H. (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys. J., 80, 2946–2953.
    • (2001) Biophys. J , vol.80 , pp. 2946-2953
    • Svergun, D.I.1    Petoukhov, M.V.2    Koch, M.H.3
  • 9
    • 23244455562 scopus 로고    scopus 로고
    • Global rigid body modeling of macromolecular complexes against small-angle scattering data
    • Petoukhov,M.V. and Svergun,D.I. (2005) Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys. J., 89, 1237–1250.
    • (2005) Biophys. J , vol.89 , pp. 1237-1250
    • Petoukhov, M.V.1    Svergun, D.I.2
  • 11
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779–815.
    • (1993) J. Mol. Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 12
    • 51249118082 scopus 로고    scopus 로고
    • Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies
    • Forster,F., Webb,B., Krukenberg,K.A., Tsuruta,H., Agard,D.A. and Sali,A. (2008) Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J. Mol. Biol., 382, 1089–1106.
    • (2008) J. Mol. Biol , vol.382 , pp. 1089-1106
    • Forster, F.1    Webb, B.2    Krukenberg, K.A.3    Tsuruta, H.4    Agard, D.A.5    Sali, A.6
  • 13
    • 77954280480 scopus 로고    scopus 로고
    • FoXS: a web server for rapid computation and fitting of SAXS profiles
    • Schneidman-Duhovny,D., Hammel,M. and Sali,A. (2010) FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res., 38, W540–W544.
    • (2010) Nucleic Acids Res , vol.38 , pp. W540-W544
    • Schneidman-Duhovny, D.1    Hammel, M.2    Sali, A.3
  • 14
    • 79851511415 scopus 로고    scopus 로고
    • Macromolecular docking restrained by a small angle X-ray scattering profile
    • Schneidman-Duhovny,D., Hammel,M. and Sali,A. (2011) Macromolecular docking restrained by a small angle X-ray scattering profile. J. Struct. Biol., 173, 461–471.
    • (2011) J. Struct. Biol , vol.173 , pp. 461-471
    • Schneidman-Duhovny, D.1    Hammel, M.2    Sali, A.3
  • 16
    • 84867508210 scopus 로고    scopus 로고
    • Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS)
    • Hammel,M. (2012) Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). Eur. Biophys. J., 41, 789–799.
    • (2012) Eur. Biophys. J , vol.41 , pp. 789-799
    • Hammel, M.1
  • 17
    • 84865525834 scopus 로고    scopus 로고
    • Integrative structural modeling with small angle X-ray scattering profiles
    • Schneidman-Duhovny,D., Kim,S.J. and Sali,A. (2012) Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct. Biol., 12, 17.
    • (2012) BMC Struct. Biol , vol.12 , pp. 17
    • Schneidman-Duhovny, D.1    Kim, S.J.2    Sali, A.3
  • 18
    • 79958045453 scopus 로고    scopus 로고
    • Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law
    • Rambo,R.P. and Tainer,J.A. (2011) Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers, 95, 559–571.
    • (2011) Biopolymers , vol.95 , pp. 559-571
    • Rambo, R.P.1    Tainer, J.A.2
  • 20
    • 77957221991 scopus 로고    scopus 로고
    • Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data
    • Pons,C., D’Abramo,M., Svergun,D.I., Orozco,M., Bernado,P. and Fernandez-Recio,J. (2010) Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. J. Mol. Biol., 403, 217–230.
    • (2010) J. Mol. Biol , vol.403 , pp. 217-230
    • Pons, C.1    D’Abramo, M.2    Svergun, D.I.3    Orozco, M.4    Bernado, P.5    Fernandez-Recio, J.6
  • 23
    • 84882940564 scopus 로고    scopus 로고
    • Accurate SAXS profile computation and its assessment by contrast variation experiments
    • Schneidman-Duhovny,D., Hammel,M., Tainer,J.A. and Sali,A. (2013) Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys. J., 105, 962–974.
    • (2013) Biophys. J , vol.105 , pp. 962-974
    • Schneidman-Duhovny, D.1    Hammel, M.2    Tainer, J.A.3    Sali, A.4
  • 24
    • 84908087566 scopus 로고
    • Zerstreuung von Röntgenstrahlen
    • Debye,P. (1915) Zerstreuung von Röntgenstrahlen. Ann. Phys., 351, 809–823.
    • (1915) Ann. Phys , vol.351 , pp. 809-823
    • Debye, P.1
  • 25
    • 33746124556 scopus 로고    scopus 로고
    • Biomolecules in the computer: Jmol to the rescue
    • Herraez,A. (2006) Biomolecules in the computer: Jmol to the rescue. Biochem. Mol. Biol. Educ., 34, 255–261.
    • (2006) Biochem. Mol. Biol. Educ , vol.34 , pp. 255-261
    • Herraez, A.1
  • 26
    • 0000988422 scopus 로고
    • Branch-and-bound methods: A survey
    • Lawler,E.L. and Wood,D.E. (1966) Branch-and-bound methods: A survey. Oper. Res., 14, 699–719.
    • (1966) Oper. Res , vol.14 , pp. 699-719
    • Lawler, E.L.1    Wood, D.E.2
  • 29
    • 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. and Sali,A. (2013) Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinformatics, 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
  • 31
    • 0036100047 scopus 로고    scopus 로고
    • Using motion planning to study protein folding pathways
    • Amato,N.M. and Song,G. (2002) Using motion planning to study protein folding pathways. J. Comput. Biol., 9, 149–168.
    • (2002) J. Comput. Biol , vol.9 , pp. 149-168
    • Amato, N.M.1    Song, G.2
  • 32
    • 29144467680 scopus 로고    scopus 로고
    • A path planning approach for computing large-amplitude motions of flexible molecules
    • (Suppl. 1)
    • Cortes,J., Simeon,T., Ruiz de Angulo,V., Guieysse,D., Remaud-Simeon,M. and Tran,V. (2005) A path planning approach for computing large-amplitude motions of flexible molecules. Bioinformatics, 21(Suppl. 1), i116–i125.
    • (2005) Bioinformatics , vol.21 , pp. i116-i125
    • Cortes, J.1    Simeon, T.2    Ruiz de Angulo, V.3    Guieysse, D.4    Remaud-Simeon, M.5    Tran, V.6
  • 33
    • 77953573815 scopus 로고    scopus 로고
    • Sub-angstrom modeling of complexes between flexible peptides and globular proteins
    • Raveh,B., London,N. and Schueler-Furman,O. (2010) Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins, 78, 2029–2040.
    • (2010) Proteins , vol.78 , pp. 2029-2040
    • Raveh, B.1    London, N.2    Schueler-Furman, O.3
  • 35
    • 84876800465 scopus 로고    scopus 로고
    • Accurate assessment of mass, models and resolution by small-angle scattering
    • Rambo,R.P. and Tainer,J.A. (2013) Accurate assessment of mass, models and resolution by small-angle scattering. Nature, 496, 477–481.
    • (2013) Nature , vol.496 , pp. 477-481
    • Rambo, R.P.1    Tainer, J.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.