메뉴 건너뛰기




Volumn 95, Issue 7, 2008, Pages 3192-3207

Damped-dynamics flexible fitting

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE (CALCIUM); ELONGATION FACTOR G; PROTEIN SERINE THREONINE KINASE;

EID: 55949095660     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.132357     Document Type: Article
Times cited : (14)

References (46)
  • 1
    • 0033863336 scopus 로고    scopus 로고
    • Domain motions of EF-G bound to the 70S ribosome: Insights from a hand-shaking between multi-resolution structures
    • Wriggers, W., R. K. Agrawal, D. L. Drew, J. A. McCammon, and J. Frank. 2000. Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures. Biophys. J. 79:1670-1678.
    • (2000) Biophys. J , vol.79 , pp. 1670-1678
    • Wriggers, W.1    Agrawal, R.K.2    Drew, D.L.3    McCammon, J.A.4    Frank, J.5
  • 2
    • 0035783173 scopus 로고    scopus 로고
    • Using Situs for flexible and rigid-body fitting of multi-resolution single-molecule data
    • Wriggers, W., and S. Birmanns. 2001. Using Situs for flexible and rigid-body fitting of multi-resolution single-molecule data. J. Struct. Biol. 133:193-202.
    • (2001) J. Struct. Biol , vol.133 , pp. 193-202
    • Wriggers, W.1    Birmanns, S.2
  • 3
    • 0034802465 scopus 로고    scopus 로고
    • Modeling tricks and fitting techniques for multi-resolution structures
    • Wriggers, W., and P. Chacón. 2001. Modeling tricks and fitting techniques for multi-resolution structures. Structure. 9:779-788.
    • (2001) Structure , vol.9 , pp. 779-788
    • Wriggers, W.1    Chacón, P.2
  • 5
    • 0742306445 scopus 로고    scopus 로고
    • Topology representing neural networks reconcile biomolecular shape, structure, and dynamics
    • Wriggers, W., P. Chacó n, J. A. Kovacs, F. Tama, and S. Birmanns. 2004. Topology representing neural networks reconcile biomolecular shape, structure, and dynamics. Neurocomputing. 56:365-379.
    • (2004) Neurocomputing , vol.56 , pp. 365-379
    • Wriggers, W.1    Chacó n, P.2    Kovacs, J.A.3    Tama, F.4    Birmanns, S.5
  • 6
    • 0036382958 scopus 로고    scopus 로고
    • Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
    • Tama, F., W. Wriggers, and C. L. Brooks. 2002. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 321:297-305.
    • (2002) J. Mol. Biol , vol.321 , pp. 297-305
    • Tama, F.1    Wriggers, W.2    Brooks, C.L.3
  • 7
    • 0037436340 scopus 로고    scopus 로고
    • MegDalton biomolecular motion captured from electron microscopy reconstructions
    • Chacón, P., F. Tama, and W. Wriggers. 2003. MegDalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol. 326:485-492.
    • (2003) J. Mol. Biol , vol.326 , pp. 485-492
    • Chacón, P.1    Tama, F.2    Wriggers, W.3
  • 8
    • 1642355235 scopus 로고    scopus 로고
    • Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis
    • Tama, F., O. Miyashita, and C. L. Brooks III. 2004a. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 337:985-999.
    • (2004) J. Mol. Biol , vol.337 , pp. 985-999
    • Tama, F.1    Miyashita, O.2    Brooks III, C.L.3
  • 9
    • 4344716056 scopus 로고    scopus 로고
    • Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
    • Tama, F., O. Miyashita, and C. L. Brooks III. 2004b. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 147:315-326.
    • (2004) J. Struct. Biol , vol.147 , pp. 315-326
    • Tama, F.1    Miyashita, O.2    Brooks III, C.L.3
  • 10
    • 2342518038 scopus 로고    scopus 로고
    • On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
    • Delarue, M., and P. Dumas. 2004. On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc. Natl. Acad. Sci. USA. 101:6957-6962.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 6957-6962
    • Delarue, M.1    Dumas, P.2
  • 11
    • 33748351384 scopus 로고    scopus 로고
    • NORMA: A tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps
    • Suhre, K., J. Navaza, and Y.-H. Sanejouand. 2006. NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta Crystallogr. D Biol. Crystallogr. 62:1098-1100.
    • (2006) Acta Crystallogr. D Biol. Crystallogr , vol.62 , pp. 1098-1100
    • Suhre, K.1    Navaza, J.2    Sanejouand, Y.-H.3
  • 12
    • 17044432465 scopus 로고    scopus 로고
    • Normal mode-based fitting of atomic structure into electron density maps: Application to sarcoplasmic reticulum CATPase
    • Hinsen, K., N. Reuter, J. Navaza, D. L. Stokes, and J.-J. Lacapère. 2005. Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum CATPase. Biophys. J. 88:818-827.
    • (2005) Biophys. J , vol.88 , pp. 818-827
    • Hinsen, K.1    Reuter, N.2    Navaza, J.3    Stokes, D.L.4    Lacapère, J.-J.5
  • 13
    • 0344120716 scopus 로고    scopus 로고
    • Low-resolution structure refinement in electron microscopy
    • Chen, J. Z., J. Fürst, M. S. Chapman, and N. Grigorieff. 2003. Low-resolution structure refinement in electron microscopy. J. Struct. Biol. 144:144-151.
    • (2003) J. Struct. Biol , vol.144 , pp. 144-151
    • Chen, J.Z.1    Fürst, J.2    Chapman, M.S.3    Grigorieff, N.4
  • 14
    • 14844311200 scopus 로고    scopus 로고
    • Fitting of high-resolution structures into electron microscopy reconstruction images
    • Fabiola, F., and M. S. Chapman. 2005. Fitting of high-resolution structures into electron microscopy reconstruction images. Structure. 13:389-400.
    • (2005) Structure , vol.13 , pp. 389-400
    • Fabiola, F.1    Chapman, M.S.2
  • 15
    • 25844459522 scopus 로고    scopus 로고
    • Combining electron microscopy and comparative protein structure modeling
    • Topf, M., and A. Sali. 2005. Combining electron microscopy and comparative protein structure modeling. Curr. Opin. Struct. Biol. 15: 578-585.
    • (2005) Curr. Opin. Struct. Biol , vol.15 , pp. 578-585
    • Topf, M.1    Sali, A.2
  • 16
    • 33645075435 scopus 로고    scopus 로고
    • Refinement of protein structures by iterative comparative modeling and cryoEM density fitting
    • Topf, M., M. L. Baker, M. A. Marti-Renom, W. Chiu, and A. Sali. 2006. Refinement of protein structures by iterative comparative modeling and cryoEM density fitting. J. Mol. Biol. 357:1655-1668.
    • (2006) J. Mol. Biol , vol.357 , pp. 1655-1668
    • Topf, M.1    Baker, M.L.2    Marti-Renom, M.A.3    Chiu, W.4    Sali, A.5
  • 18
    • 38949092920 scopus 로고    scopus 로고
    • Protein structure fitting and refinement guided by Cryo-EM density
    • Topf, M., K. Lasker, B. Webb, H. Wolfson, W. Chiu, and A. Sali. 2008. Protein structure fitting and refinement guided by Cryo-EM density. Structure. 16:295-307.
    • (2008) Structure , vol.16 , pp. 295-307
    • Topf, M.1    Lasker, K.2    Webb, B.3    Wolfson, H.4    Chiu, W.5    Sali, A.6
  • 19
    • 41449099769 scopus 로고    scopus 로고
    • Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
    • Jolley, C. C., S. A. Wells, P. Fromme, and M. F. Thorpe. 2008. Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations. Biophys. J. 94:1613-1621.
    • (2008) Biophys. J , vol.94 , pp. 1613-1621
    • Jolley, C.C.1    Wells, S.A.2    Fromme, P.3    Thorpe, M.F.4
  • 20
    • 27744471408 scopus 로고    scopus 로고
    • Constrained geometric simulation of diffusive motion in proteins
    • Wells, S., S. Menor, B. Hespenheide, and M. F. Thorpe. 2005. Constrained geometric simulation of diffusive motion in proteins. Phys. Biol. 2:S127-S136.
    • (2005) Phys. Biol , vol.2
    • Wells, S.1    Menor, S.2    Hespenheide, B.3    Thorpe, M.F.4
  • 22
    • 84986522918 scopus 로고
    • ICM: A new method for structure modeling and design: applications to docking and structure prediction from the distorted native conformation
    • Abagyan, R., M. Totrov, and D. Kuznetsov. 1994. ICM: a new method for structure modeling and design: applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 15:488-506.
    • (1994) J. Comput. Chem , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 23
    • 0024609784 scopus 로고
    • New methodology for computer-aided modeling of biomolecular structure and dynamics. 1. Non-cyclic structures
    • Mazur, A., and R. Abagyan. 1989. New methodology for computer-aided modeling of biomolecular structure and dynamics. 1. Non-cyclic structures. J. Biomol. Struct. Dyn. 6:815-832.
    • (1989) J. Biomol. Struct. Dyn , vol.6 , pp. 815-832
    • Mazur, A.1    Abagyan, R.2
  • 24
    • 0021586472 scopus 로고
    • Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles for proteins. General recurrent equations
    • Abe, H., W. Braun, T. Noguti, and N. Gō. 1984. Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles for proteins. General recurrent equations. Comput. Chem. 8:239-247.
    • (1984) Comput. Chem , vol.8 , pp. 239-247
    • Abe, H.1    Braun, W.2    Noguti, T.3    Gō, N.4
  • 25
    • 26444462147 scopus 로고    scopus 로고
    • Rapid protein side-chain packing via tree decomposition
    • Research in Computational Molecular Biology, Proceedings of the 9th Annual International Conference, RECOMB, May 14-18, of, J. P. Mesirov, S. Kasif, S. Istrail, P. A. Pevzner, and M. S. Waterman, editors. Springer-Verlag, Cambridge, MA. 2005
    • Xu, J. 2005. Rapid protein side-chain packing via tree decomposition. In Research in Computational Molecular Biology, Proceedings of the 9th Annual International Conference, RECOMB 2005, May 14-18, 2005. Vol. 3500 of Lecture Notes in Computer Science. S. Miyano, J. P. Mesirov, S. Kasif, S. Istrail, P. A. Pevzner, and M. S. Waterman, editors. Springer-Verlag, Cambridge, MA.
    • (2005) Lecture Notes in Computer Science. S. Miyano , vol.3500
    • Xu, J.1
  • 30
    • 0025968043 scopus 로고
    • SpK1, a new kinase from Saccharomyces cerevisiae, phosphorylates proteins on serine, threonine, and tyrosine
    • Stern, D. F., P. Zheng, D. R. Beidler, and C. Zerillo. 1991. SpK1, a new kinase from Saccharomyces cerevisiae, phosphorylates proteins on serine, threonine, and tyrosine. Mol. Cell. Biol. 11:987-1001.
    • (1991) Mol. Cell. Biol , vol.11 , pp. 987-1001
    • Stern, D.F.1    Zheng, P.2    Beidler, D.R.3    Zerillo, C.4
  • 31
    • 0036297629 scopus 로고    scopus 로고
    • Multi-resolution contour-based fitting of macromolecular structures
    • Chacón, P., and W. Wriggers. 2002. Multi-resolution contour-based fitting of macromolecular structures. J. Mol. Biol. 317:375-384.
    • (2002) J. Mol. Biol , vol.317 , pp. 375-384
    • Chacón, P.1    Wriggers, W.2
  • 33
  • 34
    • 33847266703 scopus 로고    scopus 로고
    • ADP-EM: Fast exhaustive multi-resolution docking for high-throughput coverage
    • Garzón, J. I., J. Kovacs, R. Abagyan, and P. Chacón. 2007. ADP-EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics. 23:427-433.
    • (2007) Bioinformatics , vol.23 , pp. 427-433
    • Garzón, J.I.1    Kovacs, J.2    Abagyan, R.3    Chacón, P.4
  • 35
    • 0034621834 scopus 로고    scopus 로고
    • Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution
    • Toyoshima, C., M. Nakasako, H. Nomura, and H. Ogawa. 2000. Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution. Nature. 405:647-655.
    • (2000) Nature , vol.405 , pp. 647-655
    • Toyoshima, C.1    Nakasako, M.2    Nomura, H.3    Ogawa, H.4
  • 36
    • 0032560170 scopus 로고    scopus 로고
    • Structure of the calcium pump from sarcoplasmic reticulum at 8 Å resolution
    • Zhang, P., C. Toyoshima, K. Yonekura, N. M. Green, and D. L. Stokes. 1998. Structure of the calcium pump from sarcoplasmic reticulum at 8 Å resolution. Nature. 392:835-839.
    • (1998) Nature , vol.392 , pp. 835-839
    • Zhang, P.1    Toyoshima, C.2    Yonekura, K.3    Green, N.M.4    Stokes, D.L.5
  • 37
    • 0027980558 scopus 로고
    • The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution
    • Czworkowski, J., J. Wang, T. A. Steitz, and P. B. Moore. 1994. The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution. EMBO J. 13:3661-3668.
    • (1994) EMBO J , vol.13 , pp. 3661-3668
    • Czworkowski, J.1    Wang, J.2    Steitz, T.A.3    Moore, P.B.4
  • 41
    • 0026544877 scopus 로고
    • 5A refined at 1.9 Å resolution. a model for a catalytic transition state
    • 5A refined at 1.9 Å resolution. a model for a catalytic transition state. J. Mol. Biol. 224:159-177.
    • (1992) J. Mol. Biol , vol.224 , pp. 159-177
    • Müller, C.W.1    Schulz, G.E.2
  • 42
    • 37349101940 scopus 로고    scopus 로고
    • An NMA- guided path planning approach for computing large-amplitude conformational changes in proteins
    • Kirillova, S., J. Cortés, A. Stefaniu, and T. Siméon. 2007. An NMA- guided path planning approach for computing large-amplitude conformational changes in proteins. Proteins Struct. Funct. Bioinf. 70: 131-143.
    • (2007) Proteins Struct. Funct. Bioinf , vol.70 , pp. 131-143
    • Kirillova, S.1    Cortés, J.2    Stefaniu, A.3    Siméon, T.4
  • 43
    • 24644483073 scopus 로고    scopus 로고
    • Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
    • Maragakis, P., and M. Karplus. 2005. Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. J. Mol. Biol. 352:807-822.
    • (2005) J. Mol. Biol , vol.352 , pp. 807-822
    • Maragakis, P.1    Karplus, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.