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Volumn 579, Issue 25, 2005, Pages 5542-5548

Validating the use of database potentials in protein structure determination by NMR

Author keywords

Database potentials of mean force; Dipolar R factor; FYVE domain; Nuclear magnetic resonance; Protein structure; Refinement; Residual dipolar couplings; Validation

Indexed keywords

PROTEIN;

EID: 26844441149     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2005.09.017     Document Type: Article
Times cited : (6)

References (30)
  • 1
    • 0029314335 scopus 로고
    • The impact of direct refinement against proton chemical shifts on protein structure determination by NMR
    • J. Kuszewski, A.M. Gronenborn, and G.M. Clore The impact of direct refinement against proton chemical shifts on protein structure determination by NMR J. Magn. Reson. Ser. B 107 1995 293 297
    • (1995) J. Magn. Reson. Ser. B , vol.107 , pp. 293-297
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 2
    • 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, and 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
  • 3
    • 0034296491 scopus 로고    scopus 로고
    • Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force
    • J. Kuszewski, and G.M. Clore Sources 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
  • 4
    • 0030339738 scopus 로고    scopus 로고
    • AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
    • R.A. Laskowski, J.A. Rullmannn, M.W. MacArthur, R. Kaptein, and J.M. Thornton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR J. Biomol. NMR 8 1996 477 486
    • (1996) J. Biomol. NMR , vol.8 , pp. 477-486
    • Laskowski, R.A.1    Rullmannn, J.A.2    MacArthur, M.W.3    Kaptein, R.4    Thornton, J.M.5
  • 5
    • 0031718310 scopus 로고    scopus 로고
    • Homology modeling, model and software evaluation: Three related resources
    • R. Rodriguez, G. Chinea, N. Lopez, T. Pons, and G. Vriend Homology modeling, model and software evaluation: three related resources Bioinformatics 14 1998 523 528
    • (1998) Bioinformatics , vol.14 , pp. 523-528
    • Rodriguez, R.1    Chinea, G.2    Lopez, N.3    Pons, T.4    Vriend, G.5
  • 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. Graph. 8 1990 52 56
    • (1990) J Mol. Graph. , vol.8 , pp. 52-56
    • Vriend, G.1
  • 8
    • 0032879507 scopus 로고    scopus 로고
    • R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures
    • G.M. Clore, and 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
  • 9
    • 0032528033 scopus 로고    scopus 로고
    • Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
    • G. Cornilescu, J.L. Marquardt, M. Ottiger, and A. Bax Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase J. Am. Chem. Soc. 120 1998 6836 6837
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 6836-6837
    • Cornilescu, G.1    Marquardt, J.L.2    Ottiger, M.3    Bax, A.4
  • 10
    • 0037433242 scopus 로고    scopus 로고
    • Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation
    • G.M. Clore, and J. Kuszewski Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation J. Am. Chem. Soc. 125 2003 1518 1525
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1518-1525
    • Clore, G.M.1    Kuszewski, J.2
  • 11
    • 0036219167 scopus 로고    scopus 로고
    • Improving the quality of protein structures derived by NMR spectroscopy
    • C.A. Spronk, J.P. Linge, C.W. Hilbers, and G.W. Vuister Improving the quality of protein structures derived by NMR spectroscopy J. Biomol. NMR 22 2002 281 289
    • (2002) J. Biomol. NMR , vol.22 , pp. 281-289
    • Spronk, C.A.1    Linge, J.P.2    Hilbers, C.W.3    Vuister, G.W.4
  • 13
    • 0033064496 scopus 로고    scopus 로고
    • Influence of non-bonded parameters on the quality of NMR structures: A new force field for NMR structure calculation
    • J.P. Linge, and M. Nilges Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation J. Biomol. NMR 13 1999 51 59
    • (1999) J. Biomol. NMR , vol.13 , pp. 51-59
    • Linge, J.P.1    Nilges, M.2
  • 16
    • 0031627465 scopus 로고    scopus 로고
    • An efficient and cost-effective isotope labeling protocol for proteins expressed in Escherichia coli
    • M.L. Cai, Y. Huang, K. Sakaguchi, G.M. Clore, A.M. Gronenborn, and R. Craigie An efficient and cost-effective isotope labeling protocol for proteins expressed in Escherichia coli J. Biomol. NMR 11 1998 97 102
    • (1998) J. Biomol. NMR , vol.11 , pp. 97-102
    • Cai, M.L.1    Huang, Y.2    Sakaguchi, K.3    Clore, G.M.4    Gronenborn, A.M.5    Craigie, R.6
  • 17
    • 0034130999 scopus 로고    scopus 로고
    • Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions
    • M.R. Hansen, P. Hanson, and A. Pardi Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions Meth. Enzymol. 317 2000 220 240
    • (2000) Meth. Enzymol. , vol.317 , pp. 220-240
    • Hansen, M.R.1    Hanson, P.2    Pardi, A.3
  • 18
    • 0032556228 scopus 로고    scopus 로고
    • Single scan, sensitivity- and gradient-enhanced TROSY for multidimensional NMR experiments
    • J. Weigelt Single scan, sensitivity- and gradient-enhanced TROSY for multidimensional NMR experiments J. Am. Chem. Soc. 120 1998 10778 10779
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 10778-10779
    • Weigelt, J.1
  • 19
    • 0034003170 scopus 로고    scopus 로고
    • Transverse relaxation optimised spin-state selective NMR experiments for measurement of residual dipolar couplings
    • P. Permi, and A. Annila Transverse relaxation optimised spin-state selective NMR experiments for measurement of residual dipolar couplings J. Biomol. NMR 16 2000 221 227
    • (2000) J. Biomol. NMR , vol.16 , pp. 221-227
    • Permi, P.1    Annila, A.2
  • 21
    • 26844531644 scopus 로고    scopus 로고
    • University of California, San Francisco.
    • Goddard, T.D. and Kneller, D.G. University of California, San Francisco.
    • Goddard, T.D.1    Kneller, D.G.2
  • 22
    • 0034792548 scopus 로고    scopus 로고
    • Direct structure refinement of high molecular weight proteins against residual dipolar couplings and carbonyl chemical shift changes upon alignment: An application to maltose binding protein
    • W.Y. Choy, M. Tollinger, G.A. Mueller, and L.E. Kay Direct structure refinement of high molecular weight proteins against residual dipolar couplings and carbonyl chemical shift changes upon alignment: an application to maltose binding protein J. Biomol. NMR 21 2001 31 40
    • (2001) J. Biomol. NMR , vol.21 , pp. 31-40
    • Choy, W.Y.1    Tollinger, M.2    Mueller, G.A.3    Kay, L.E.4
  • 23
    • 0030621858 scopus 로고    scopus 로고
    • Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation
    • E.G. Stein, L.M. Rice, and A.T. Brunger Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation J. Magn. Reson. 124 1997 154 164
    • (1997) J. Magn. Reson. , vol.124 , pp. 154-164
    • Stein, E.G.1    Rice, L.M.2    Brunger, A.T.3
  • 24
    • 0034486021 scopus 로고    scopus 로고
    • Solution structure of DinI provides insight into its mode of RecA inactivation
    • B.E. Ramirez, O.N. Voloshin, R.D. Camerini-Otero, and A. Bax Solution structure of DinI provides insight into its mode of RecA inactivation Protein Sci. 9 2000 2161 2169
    • (2000) Protein Sci. , vol.9 , pp. 2161-2169
    • Ramirez, B.E.1    Voloshin, O.N.2    Camerini-Otero, R.D.3    Bax, A.4
  • 25
    • 4644237840 scopus 로고    scopus 로고
    • Three-dimensional solution structure of the cytoplasmic B domain of the mannitol transporter IImannitol of the Escherichia coli phosphotransferase system
    • P.M. Legler, M. Cai, A. Peterkofsky, and G.M. Clore Three-dimensional solution structure of the cytoplasmic B domain of the mannitol transporter IImannitol of the Escherichia coli phosphotransferase system J. Biol. Chem. 279 2004 39115 39121
    • (2004) J. Biol. Chem. , vol.279 , pp. 39115-39121
    • Legler, P.M.1    Cai, M.2    Peterkofsky, A.3    Clore, G.M.4
  • 26
    • 0033054043 scopus 로고    scopus 로고
    • High precision solution structure of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, a c-myc transcription factor
    • J.L. Baber, D. Libutti, D. Levens, and N. Tjandra High precision solution structure of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, a c-myc transcription factor J. Mol. Biol. 289 1999 949 962
    • (1999) J. Mol. Biol. , vol.289 , pp. 949-962
    • Baber, J.L.1    Libutti, D.2    Levens, D.3    Tjandra, N.4
  • 27
    • 0033145058 scopus 로고    scopus 로고
    • Order matrix analysis of residual dipolar couplings using singular value decomposition
    • J.A. Losonczi, M. Andrec, M.W. Fischer, and J.H. Prestegard Order matrix analysis of residual dipolar couplings using singular value decomposition J. Magn. Reson. 138 1999 334 342
    • (1999) J. Magn. Reson. , vol.138 , pp. 334-342
    • Losonczi, J.A.1    Andrec, M.2    Fischer, M.W.3    Prestegard, J.H.4
  • 28
    • 0034685436 scopus 로고    scopus 로고
    • Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR
    • M. Zweckstetter, and A. Bax Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR J. Am. Chem. Soc. 122 2000 3791 3792
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 3791-3792
    • Zweckstetter, M.1    Bax, A.2
  • 30
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • R. Koradi, M. Billeter, and K. Wuthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph. 14 1996 51 55
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.