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Volumn 149, Issue 2, 2001, Pages 239-244

The VMD-XPLOR visualization package for NMR structure refinement

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; G SUBSTRATE; G-SUBSTRATE; NERVE PROTEIN; PHOSPHOCARRIER PROTEIN HPR; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE;

EID: 0035742163     PISSN: 10907807     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmre.2001.2300     Document Type: Article
Times cited : (114)

References (37)
  • 1
    • 85120226940 scopus 로고
    • A.T. Brünger XPLOR Manual Version 3.1 1993 Yale Univ. Press New Haven
    • (1993)
    • Brünger, A.T.1
  • 3
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program Dyana
    • P. Güntert C. Mumenthaler K. Wüthrich Torsion angle dynamics for NMR structure calculation with the new program Dyana J. Mol. Biol. 273 1997 283 298
    • (1997) J. Mol. Biol. , vol.273 , pp. 283-298
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 4
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • R. Koradi M. Billeter K. Wuthrich MOLMOL: A program for display and analysis of macromolecular structures J. Mol. Graphics 14 1996 51 55
    • (1996) J. Mol. Graphics , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 5
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from interfacial and thermodynamic properties of hydrocarbons
    • A. Nicholls K.A. Sharp B. Honig Protein folding and association: Insights from interfacial and thermodynamic properties of hydrocarbons Proteins 11 1991 281 296
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 7
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • G. Vriend WHAT IF: A molecular modeling and drug design program J. Mol. Graphics 8 1990 52 56
    • (1990) J. Mol. Graphics , vol.8 , pp. 52-56
    • Vriend, G.1
  • 9
    • 85120213395 scopus 로고    scopus 로고
    • A. T. Brünger, and, W. L. DeLano, unpublished.
  • 10
    • 85120226662 scopus 로고    scopus 로고
    • W. Humphrey, A. Dalke, and, K. Schulten, VMD—Visual molecular dynamics, J. Mol. Graphics, 14, 33, – 38, (1996). “Available online at, http://www.ks.uiuc.edu/Research/vmd/ , ”
  • 11
    • 0022357843 scopus 로고
    • The solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli: Combined use of 1H-nuclear magnetic resonance and restrained molecular dynamics
    • 1H-nuclear magnetic resonance and restrained molecular dynamics J. Mol. Biol. 186 1985 435 455
    • (1985) J. Mol. Biol. , vol.186 , pp. 435-455
    • Clore, G.M.1    Gronenborn, A.M.2    Brünger, A.T.3    Karplus, M.4
  • 12
    • 0023008905 scopus 로고
    • Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: A model study of crambin
    • G.M. Clore A.T. Brünger M. Karplus A.M. Gronenborn Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: A model study of crambin J. Mol. Biol. 191 1986 523 551
    • (1986) J. Mol. Biol. , vol.191 , pp. 523-551
    • Clore, G.M.1    Brünger, A.T.2    Karplus, M.3    Gronenborn, A.M.4
  • 13
    • 0024285896 scopus 로고
    • Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry–dynamical simulated annealing calculations
    • M. Nilges G.M. Clore A.M. Gronenborn Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry–dynamical simulated annealing calculations FEBS Lett. 229 1988 317 324
    • (1988) FEBS Lett. , vol.229 , pp. 317-324
    • Nilges, M.1    Clore, G.M.2    Gronenborn, A.M.3
  • 14
    • 0023998438 scopus 로고
    • Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2
    • M. Nilges A.M. Gronenborn A.T. Brünger G.M. Clore Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2 Protein Eng. 2 1988 27 38
    • (1988) Protein Eng. , vol.2 , pp. 27-38
    • Nilges, M.1    Gronenborn, A.M.2    Brünger, A.T.3    Clore, G.M.4
  • 15
    • 0023140814 scopus 로고
    • Crystallographic R-factor refinement by molecular dynamics
    • A.T. Brünger J. Kuryan M. Karplus Crystallographic R-factor refinement by molecular dynamics Science 235 1986 458 460
    • (1986) Science , vol.235 , pp. 458-460
    • Brünger, A.T.1    Kuryan, J.2    Karplus, M.3
  • 16
    • 0032568556 scopus 로고    scopus 로고
    • New methods of structure refinement for macromolecular structure determination by NMR
    • G.M. Clore A.M. Gronenborn New methods of structure refinement for macromolecular structure determination by NMR Proc. Natl. Acad. Sci. USA 95 1998 5891 5898
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5891-5898
    • Clore, G.M.1    Gronenborn, A.M.2
  • 19
    • 0029314335 scopus 로고
    • The impact of direct refinement against proton chemical shifts in protein structure determination by NMR
    • J. Kuszewski A.M. Gronenborn G.M. Clore The impact of direct refinement against proton chemical shifts in protein structure determination by NMR J. Magn. Reson. B 107 1995 293 297
    • (1995) J. Magn. Reson. B , vol.107 , pp. 293-297
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 20
    • 0030191673 scopus 로고    scopus 로고
    • A potential involving multiple proton chemical shift restraints for non-stereospecifically assigned methyl and methylene protons
    • J. Kuszewski A.M. Gronenborn G.M. Clore A potential involving multiple proton chemical shift restraints for non-stereospecifically assigned methyl and methylene protons J. Magn. Reson. B 112 1996 79 81
    • (1996) J. Magn. Reson. B , vol.112 , pp. 79-81
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 22
    • 0032012610 scopus 로고
    • Direct refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude
    • G.M. Clore A.M. Gronenborn N. Tjandra Direct refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude J. Magn. Reson. 131 1988 159 162
    • (1988) J. Magn. Reson. , vol.131 , pp. 159-162
    • Clore, G.M.1    Gronenborn, A.M.2    Tjandra, N.3
  • 23
    • 0034132563 scopus 로고    scopus 로고
    • Direct refinement against proton–proton dipolar couplings in NMR structure determination of macromolecules
    • N. Tjandra J. Marquardt G.M. Clore Direct refinement against proton–proton dipolar couplings in NMR structure determination of macromolecules J. Magn. Reson. 142 2000 393 396
    • (2000) J. Magn. Reson. , vol.142 , pp. 393-396
    • Tjandra, N.1    Marquardt, J.2    Clore, G.M.3
  • 24
    • 0030000912 scopus 로고    scopus 로고
    • Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases
    • J. Kuszewski A.M. Gronenborn G.M. Clore Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases Protein Sci. 5 1996 1067 1080
    • (1996) Protein Sci. , vol.5 , pp. 1067-1080
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 25
    • 0031083293 scopus 로고    scopus 로고
    • Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids
    • J. Kuszewski A.M. Gronenborn G.M. Clore Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids J. Magn. Reson. 125 1997 171 188
    • (1997) J. Magn. Reson. , vol.125 , pp. 171-188
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 26
    • 0034296491 scopus 로고    scopus 로고
    • Source of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force
    • J. Kuszewski G.M. Clore Source of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force J. Magn. Reson. 146 2000 249 254
    • (2000) J. Magn. Reson. , vol.146 , pp. 249-254
    • Kuszewski, J.1    Clore, G.M.2
  • 27
    • 85120194821 scopus 로고    scopus 로고
    • Available online at, http://atb.csb.yale.edu/xplor/ .
  • 28
    • 85120200588 scopus 로고    scopus 로고
    • Available online at, ftp://portal.niddk.nih.gov/pub/clore/xplor_nih .
  • 29
    • 85120205032 scopus 로고    scopus 로고
    • J. K. Ousterhout, Tcl and the Tk Toolkit, Addison–Wesley, Reading, MA, 1994.
  • 30
    • 0032939176 scopus 로고    scopus 로고
    • Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr
    • D.S. Garrett Y.J. Seok A. Peterkofsky A.M. Gronnenborn G.M. Clore Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr Nat. Struct. Biol. 6 1999 166 173
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 166-173
    • Garrett, D.S.1    Seok, Y.J.2    Peterkofsky, A.3    Gronnenborn, A.M.4    Clore, G.M.5
  • 33
    • 0344258272 scopus 로고    scopus 로고
    • Impact of residual dipolar couplings on the accuracy of NMR structures determined from a minimal number of NOE restraints
    • G.M. Clore M.R. Starich C.A. Bewley M. Cai J. Kuszewski Impact of residual dipolar couplings on the accuracy of NMR structures determined from a minimal number of NOE restraints J. Am. Chem. Soc. 121 1999 6513 6514
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 6513-6514
    • Clore, G.M.1    Starich, M.R.2    Bewley, C.A.3    Cai, M.4    Kuszewski, J.5
  • 34
    • 0032879507 scopus 로고    scopus 로고
    • R-factor, free R and complete cross-validation for dipolar coupling refinement of NMR structures
    • G.M. Clore D.S. Garrett R-factor, free R and complete cross-validation for dipolar coupling refinement of NMR structures J. Am. Chem. Soc. 121 1999 9008 9012
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 9008-9012
    • Clore, G.M.1    Garrett, D.S.2
  • 35
    • 0034620764 scopus 로고    scopus 로고
    • Protein structure determination using molecular fragment replacement and NMR dipolar couplings
    • F. Delaglio G. Kontaxis A. Bax Protein structure determination using molecular fragment replacement and NMR dipolar couplings J. Am. Chem. Soc. 122 2000 2142 2143
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2142-2143
    • Delaglio, F.1    Kontaxis, G.2    Bax, A.3
  • 36
    • 0034254909 scopus 로고    scopus 로고
    • Accurate and rapid docking of protein–protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization
    • G.M. Clore Accurate and rapid docking of protein–protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization Proc. Natl. Acad. Sci. USA 97 2000 9021 9025
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 9021-9025
    • Clore, G.M.1
  • 37
    • 0034725409 scopus 로고    scopus 로고
    • Determination of the relative orientation of the two halves of the domain-swapped dimer of cyanovirin-N in solution using dipolar couplings and rigid body minimization
    • C.A. Bewley G.M. Clore Determination of the relative orientation of the two halves of the domain-swapped dimer of cyanovirin-N in solution using dipolar couplings and rigid body minimization J. Am. Chem. Soc. 122 2000 6009 6016
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 6009-6016
    • Bewley, C.A.1    Clore, G.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.