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Volumn 133, Issue 2-3, 2001, Pages 193-202

Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data

Author keywords

Docking; Induced fit; Macromolecular assemblies; Topology representing neural networks; Visualization; Volumetric registration

Indexed keywords

ACTIN; ISOPROTEIN; LACTOFERRIN;

EID: 0035783173     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.2000.4350     Document Type: Conference Paper
Times cited : (203)

References (20)
  • 1
    • 0032809077 scopus 로고    scopus 로고
    • Low-resolution density maps from atomic models: How stepping "back" can be a step "forward."
    • Belnap, D. M., Kumar, A., Folk, J. T., Smith, T. J., and Baker, T. S. (1999) Low-resolution density maps from atomic models: How stepping "back" can be a step "forward." J. Struct. Biol. 125, 166-175.
    • (1999) J. Struct. Biol. , vol.125 , pp. 166-175
    • Belnap, D.M.1    Kumar, A.2    Folk, J.T.3    Smith, T.J.4    Baker, T.S.5
  • 3
    • 0003769049 scopus 로고
    • The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University
    • Brünger, A. (1992) X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University.
    • (1992) X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR
    • Brünger, A.1
  • 4
    • 0034705330 scopus 로고    scopus 로고
    • Reconstruction of protein form with X-ray solution scattering and a genetic algorithm
    • Chacón, P., Díaz, J. F., Morán, F., and Andreu, J. M. (2000) Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. J. Mol. Biol. 299, 1289-1302.
    • (2000) J. Mol. Biol. , vol.299 , pp. 1289-1302
    • Chacón, P.1    Díaz, J.F.2    Morán, F.3    Andreu, J.M.4
  • 5
    • 0011943096 scopus 로고    scopus 로고
    • ADF stabilizes an existing state of F-actin and can change the tilt of F-actin subunits
    • Galkin, V. E., Orlova, A., Lukoyanova, N., Wriggers, W., and Egelman, E. H. ADF stabilizes an existing state of F-actin and can change the tilt of F-actin subunits. J. Cell Biol. 153, 77-86.
    • J. Cell Biol. , vol.153 , pp. 77-86
    • Galkin, V.E.1    Orlova, A.2    Lukoyanova, N.3    Wriggers, W.4    Egelman, E.H.5
  • 6
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • Gerstein, M., and Krebs, W. (1998) A database of macromolecular motions. Nucleic Acids Res. 26, 4280-4290.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2
  • 7
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein, M., Lesk, A. M., and Chothia, C. (1994) Structural mechanisms for domain movements in proteins. Biochemistry 33, 6739-6749.
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 9
    • 0034695259 scopus 로고    scopus 로고
    • 15 Å resolution model of the monomeric kinesin motor, KIF1A
    • Kikkawa, M., Okada, Y., and Hirokawa, N. (2000) 15 Å resolution model of the monomeric kinesin motor, KIF1A. Cell 100, 241-252.
    • (2000) Cell , vol.100 , pp. 241-252
    • Kikkawa, M.1    Okada, Y.2    Hirokawa, N.3
  • 12
    • 0034708341 scopus 로고    scopus 로고
    • Structure of the utrophin actin-binding domain bound to F-actin reveals binding by an induced fit mechanism
    • Moores, C. A., Keep, N. H., and Kendrick-Jones, J. (2000) Structure of the utrophin actin-binding domain bound to F-actin reveals binding by an induced fit mechanism. J. Mol. Biol. 297, 465-480.
    • (2000) J. Mol. Biol. , vol.297 , pp. 465-480
    • Moores, C.A.1    Keep, N.H.2    Kendrick-Jones, J.3
  • 13
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys. 23, 327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 15
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • van Gunsteren, W. F., and Berendsen, H. J. C. (1977) Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34, 1311-1327.
    • (1977) Mol. Phys. , vol.34 , pp. 1311-1327
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 16
    • 0039807844 scopus 로고    scopus 로고
    • Using Situs for the registration of protein structures with low-resolution bead models from X-ray solution scattering
    • in press
    • Wriggers, W., and Chacón, P. Using Situs for the registration of protein structures with low-resolution bead models from X-ray solution scattering. J. Appl. Cryst., in press.
    • J. Appl. Cryst.
    • Wriggers, W.1    Chacón, P.2
  • 17
    • 0033136019 scopus 로고    scopus 로고
    • Investigating a back door mechanism of actin phosphate release by steered molecular dynamics
    • Wriggers, W., and Schulten, K. (1999) Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Proteins Struct. Function Genet. 35, 262-273.
    • (1999) Proteins Struct. Function Genet. , vol.35 , pp. 262-273
    • Wriggers, W.1    Schulten, K.2
  • 18
    • 0032545184 scopus 로고    scopus 로고
    • Self-organizing neural networks bridge the biomolecular resolution gap
    • Wriggers, W., Milligan, R. A., Schulten, K., and McCammon, J. A. (1998) Self-organizing neural networks bridge the biomolecular resolution gap. J. Mol. Biol. 284, 1247-1254.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1247-1254
    • Wriggers, W.1    Milligan, R.A.2    Schulten, K.3    McCammon, J.A.4
  • 19
    • 0032780181 scopus 로고    scopus 로고
    • Situs: A package for docking crystal structures into low-resolution maps from electron microscopy
    • Wriggers, W., Milligan, R. A., and McCammon, J. A. (1999) Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125, 185-195.
    • (1999) J. Struct. Biol. , vol.125 , pp. 185-195
    • Wriggers, W.1    Milligan, R.A.2    McCammon, J.A.3
  • 20
    • 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., Agrawal, R. K., Drew, D. L., McCammon, J. A., and Frank, J. (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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.