메뉴 건너뛰기




Volumn 43, Issue W1, 2015, Pages W356-W361

PyDockSAXS: Protein-protein complex structure by SAXS and computational docking

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; AUTOMATION; COMPUTER INTERFACE; DATA ANALYSIS; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MOLECULAR DOCKING; MOLECULAR MODEL; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SCORING SYSTEM; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY; CHEMISTRY; COMPUTER PROGRAM; INTERNET; PROCEDURES; SMALL ANGLE SCATTERING; X RAY DIFFRACTION;

EID: 84979865123     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv368     Document Type: Article
Times cited : (58)

References (42)
  • 1
    • 0032943195 scopus 로고    scopus 로고
    • Grasping at molecular interactions and genetic networks in drosophila melanogaster using fly nets, an internet database
    • Sanchez, C., Lachaize, C., Janody, F., Bellon, B., Roder, L., Euzenat, J., Rechenmann, F. and Jacq, B. (1999) Grasping at molecular interactions and genetic networks in Drosophila melanogaster using Fly Nets, an Internet database. Nucleic Acids Res., 27, 89-94.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 89-94
    • Sanchez, C.1    Lachaize, C.2    Janody, F.3    Bellon, B.4    Roder, L.5    Euzenat, J.6    Rechenmann, F.7    Jacq, B.8
  • 2
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. and Bork, P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 3
    • 84871967106 scopus 로고    scopus 로고
    • Interactome3D: Adding structural details to protein networks
    • Mosca, R., Ceol, A. and Aloy, P. (2013) Interactome3D: adding structural details to protein networks. Nat. Methods, 10, 47-53.
    • (2013) Nat. Methods , vol.10 , pp. 47-53
    • Mosca, R.1    Ceol, A.2    Aloy, P.3
  • 4
    • 84918778530 scopus 로고    scopus 로고
    • High-throughput studies of protein shapes and interactions by synchrotron small-angle X-ray scattering
    • Jeffries, C.M. and Svergun, D.I. (2015) High-throughput studies of protein shapes and interactions by synchrotron small-angle X-ray scattering. Methods Mol. Biol., 1261, 277-301.
    • (2015) Methods Mol. Biol. , vol.1261 , pp. 277-301
    • Jeffries, C.M.1    Svergun, D.I.2
  • 5
    • 84859266852 scopus 로고    scopus 로고
    • Low-resolution structural approaches to study biomolecular assemblies
    • Bernadó, P. (2011) Low-resolution structural approaches to study biomolecular assemblies. WIRES Comput. Mol. Sci., 1, 283-297.
    • (2011) WIRES Comput. Mol. Sci. , vol.1 , pp. 283-297
    • Bernadó, P.1
  • 6
    • 0345169163 scopus 로고    scopus 로고
    • Small-angle scattering: A view on the properties, structures and structural changes of biological macromolecules in solution
    • Koch, M.H., Vachette, P. and Svergun, D.I. (2003) Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q. Rev. Biophys., 36, 147-227.
    • (2003) Q. Rev. Biophys. , vol.36 , pp. 147-227
    • Koch, M.H.1    Vachette, P.2    Svergun, D.I.3
  • 7
    • 77956190770 scopus 로고    scopus 로고
    • Structural characterization of proteins and complexes using small-angle X-ray solution scattering
    • Mertens, H.D. and Svergun, D.I. (2010) Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J. Struct. Biol., 172, 128-141.
    • (2010) J. Struct. Biol. , vol.172 , pp. 128-141
    • Mertens, H.D.1    Svergun, D.I.2
  • 8
    • 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
  • 9
    • 77950223101 scopus 로고    scopus 로고
    • Small-angle scattering for structural biology-expanding the frontier while avoiding the pitfalls
    • Jacques, D.A. and Trewhella, J. (2010) Small-angle scattering for structural biology-expanding the frontier while avoiding the pitfalls. Protein Sci., 19, 642-657.
    • (2010) Protein Sci. , vol.19 , pp. 642-657
    • Jacques, D.A.1    Trewhella, J.2
  • 10
    • 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
    • 17344380633 scopus 로고    scopus 로고
    • ICM-DISCO docking by global energy optimization with fully flexible side-chains
    • Fernandez-Recio, J., Totrov, M. and Abagyan, R. (2003) ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins, 52, 113-117.
    • (2003) Proteins , vol.52 , pp. 113-117
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 12
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith, G.R. and Sternberg, M.J. (2002) Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol., 12, 28-35.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 13
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin, A.M. (2006) Flexible protein-protein docking. Curr. Opin. Struct. Biol., 16, 194-200.
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 194-200
    • Bonvin, A.M.1
  • 14
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • Gray, J.J. (2006) High-resolution protein-protein docking. Curr. Opin. Struct. Biol., 16, 183-193.
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 183-193
    • Gray, J.J.1
  • 15
    • 41949111630 scopus 로고    scopus 로고
    • Recent progress and future directions in protein-protein docking
    • Ritchie, D.W. (2008) Recent progress and future directions in protein-protein docking. Curr. Protein Pept. Sci., 9, 1-15.
    • (2008) Curr. Protein Pept. Sci. , vol.9 , pp. 1-15
    • Ritchie, D.W.1
  • 16
    • 34250882254 scopus 로고    scopus 로고
    • Pydock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
    • Cheng, T.M., Blundell, T.L. and Fernandez-Recio, J. (2007) Pydock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins, 68, 503-515.
    • (2007) Proteins , vol.68 , pp. 503-515
    • Cheng, T.M.1    Blundell, T.L.2    Fernandez-Recio, J.3
  • 17
    • 21644447570 scopus 로고    scopus 로고
    • Improving CAPRI predictions: Optimized desolvation for rigid-body docking
    • Fernandez-Recio, J., Abagyan, R. and Totrov, M. (2005) Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins, 60, 308-313.
    • (2005) Proteins , vol.60 , pp. 308-313
    • Fernandez-Recio, J.1    Abagyan, R.2    Totrov, M.3
  • 18
  • 19
    • 77957950490 scopus 로고    scopus 로고
    • Optimization of Pydock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding
    • Pons, C., Solernou, A., Perez-Cano, L., Grosdidier, S. and Fernandez-Recio, J. (2010) Optimization of Pydock for the new CAPRI challenges: docking of homology-based models, domain-domain assembly and protein-RNA binding. Proteins, 78, 3182-3188.
    • (2010) Proteins , vol.78 , pp. 3182-3188
    • Pons, C.1    Solernou, A.2    Perez-Cano, L.3    Grosdidier, S.4    Fernandez-Recio, J.5
  • 20
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez, C., Boelens, R. and Bonvin, A.M. (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc., 125, 1731-1737.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 21
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • Mendez, R., Leplae, R., De Maria, L. and Wodak, S.J. (2003) Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins, 52, 51-67.
    • (2003) Proteins , vol.52 , pp. 51-67
    • Mendez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 22
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Mendez, R., Leplae, R., Lensink, M.F. and Wodak, S.J. (2005) Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins, 60, 150-169.
    • (2005) Proteins , vol.60 , pp. 150-169
    • Mendez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 23
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd Edition
    • Lensink, M.F., Mendez, R. and Wodak, S.J. (2007) Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins, 69, 704-718.
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1    Mendez, R.2    Wodak, S.J.3
  • 24
    • 77957934896 scopus 로고    scopus 로고
    • Docking and scoring protein interactions: CAPRI 2009
    • Lensink, M.F. and Wodak, S.J. (2010) Docking and scoring protein interactions: CAPRI 2009. Proteins, 78, 3073-3084.
    • (2010) Proteins , vol.78 , pp. 3073-3084
    • Lensink, M.F.1    Wodak, S.J.2
  • 25
    • 84888289172 scopus 로고    scopus 로고
    • Docking, scoring, and affinity prediction in CAPRI
    • Lensink, M.F. and Wodak, S.J. (2013) Docking, scoring, and affinity prediction in CAPRI. Proteins, 81, 2082-2095.
    • (2013) Proteins , vol.81 , pp. 2082-2095
    • Lensink, M.F.1    Wodak, S.J.2
  • 26
    • 33645095436 scopus 로고    scopus 로고
    • Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment
    • Chelliah, V., Blundell, T.L. and Fernandez-Recio, J. (2006) Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. J. Mol. Biol., 357, 1669-1682.
    • (2006) J. Mol. Biol. , vol.357 , pp. 1669-1682
    • Chelliah, V.1    Blundell, T.L.2    Fernandez-Recio, J.3
  • 27
    • 28044449725 scopus 로고    scopus 로고
    • Computational docking and solution x-ray scattering predict a membrane-interacting role for the histone domain of the Ras activator son of sevenless
    • Sondermann, H., Nagar, B., Bar-Sagi, D. and Kuriyan, J. (2005) Computational docking and solution x-ray scattering predict a membrane-interacting role for the histone domain of the Ras activator son of sevenless. Proc. Natl. Acad. Sci. U.S.A., 102, 16632-16637.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 16632-16637
    • Sondermann, H.1    Nagar, B.2    Bar-Sagi, D.3    Kuriyan, J.4
  • 28
    • 63449120449 scopus 로고    scopus 로고
    • Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering
    • Bernado, P., Perez, Y., Blobel, J., Fernandez-Recio, J., Svergun, D.I. and Pons, M. (2009) Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering. Protein Sci., 18, 716-726.
    • (2009) Protein Sci. , vol.18 , pp. 716-726
    • Bernado, P.1    Perez, Y.2    Blobel, J.3    Fernandez-Recio, J.4    Svergun, D.I.5    Pons, M.6
  • 29
    • 70350721626 scopus 로고    scopus 로고
    • Binding of rabies virus polymerase cofactor to recombinant circular nucleoprotein-RNA complexes
    • Ribeiro Ede, A. Jr, Leyrat, C., Gerard, F.C., Albertini, A.A., Falk, C., Ruigrok, R.W. and Jamin, M. (2009) Binding of rabies virus polymerase cofactor to recombinant circular nucleoprotein-RNA complexes. J. Mol. Biol., 394, 558-575.
    • (2009) J. Mol. Biol. , vol.394 , pp. 558-575
    • Ribeiro-Ede, A.1    Leyrat, C.2    Gerard, F.C.3    Albertini, A.A.4    Falk, C.5    Ruigrok, R.W.6    Jamin, M.7
  • 31
    • 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
  • 32
    • 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
  • 33
    • 84877278835 scopus 로고    scopus 로고
    • On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys
    • Karaca, E. and Bonvin, A.M. (2013) On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys. Acta Crystallogr. D Biol. Crystallogr., 69, 683-694.
    • (2013) Acta Crystallogr. D Biol. Crystallogr. , vol.69 , pp. 683-694
    • Karaca, E.1    Bonvin, A.M.2
  • 34
    • 0029185933 scopus 로고
    • CRYSOL-A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
    • Svergun, D.I., Barberato, C. and Koch, M.H.J. (1995) CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr., 28, 768-773.
    • (1995) J. Appl. Crystallogr. , vol.28 , pp. 768-773
    • Svergun, D.I.1    Barberato, C.2    Koch, M.H.J.3
  • 35
    • 77957944014 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 4.0
    • Hwang, H., Vreven, T., Janin, J. and Weng, Z. (2010) Protein-protein docking benchmark version 4.0. Proteins, 78, 3111-3114.
    • (2010) Proteins , vol.78 , pp. 3111-3114
    • Hwang, H.1    Vreven, T.2    Janin, J.3    Weng, Z.4
  • 36
    • 58549114655 scopus 로고    scopus 로고
    • Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: Structures, stability, mechanism, and insights into amyotrophic lateral sclerosis
    • Shin, D.S., Didonato, M., Barondeau, D.P., Hura, G.L., Hitomi, C., Berglund, J.A., Getzoff, E.D., Cary, S.C. and Tainer, J.A. (2009) Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis. J. Mol. Biol., 385, 1534-1555.
    • (2009) J. Mol. Biol. , vol.385 , pp. 1534-1555
    • Shin, D.S.1    Didonato, M.2    Barondeau, D.P.3    Hura, G.L.4    Hitomi, C.5    Berglund, J.A.6    Getzoff, E.D.7    Cary, S.C.8    Tainer, J.A.9
  • 38
    • 43949086199 scopus 로고    scopus 로고
    • Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy
    • Xu, X., Reinle, W., Hannemann, F., Konarev, P.V., Svergun, D.I., Bernhardt, R. and Ubbink, M. (2008) Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy. J. Am. Chem. Soc., 130, 6395-6403.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 6395-6403
    • Xu, X.1    Reinle, W.2    Hannemann, F.3    Konarev, P.V.4    Svergun, D.I.5    Bernhardt, R.6    Ubbink, M.7
  • 41
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu, A.A., Shelenkov, A.A. and Dunbrack, R.L. Jr (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci., 12, 2001-2014.
    • (2003) Protein Sci. , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack, R.L.3
  • 42
    • 84879916282 scopus 로고    scopus 로고
    • Pydock WEB: A web server for rigid-body protein-protein docking using electrostatics and desolvation scoring
    • Jimenez-Garcia, B., Pons, C. and Fernandez-Recio, J. (2013) Pydock WEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. Bioinformatics, 29, 1698-1699.
    • (2013) Bioinformatics , vol.29 , pp. 1698-1699
    • Jimenez-Garcia, B.1    Pons, C.2    Fernandez-Recio, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.