메뉴 건너뛰기




Volumn 364, Issue , 2007, Pages 255-272

Quality control and validation

(1)  Kleywegt, Gerard J a  

a NONE

Author keywords

Electron density; Model bias; Model building; Protein structure; Quality control; Ramachandran plot; Refinement; Structure; Validation; X ray crystallography

Indexed keywords

PROTEIN;

EID: 36549052564     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-266-1:255     Document Type: Article
Times cited : (11)

References (60)
  • 1
    • 0001644632 scopus 로고
    • Between objectivity and subjectivity
    • Brändén, C. I. and Jones, T. A. (1990) Between objectivity and subjectivity. Nature 343, 687-689.
    • (1990) Nature , vol.343 , pp. 687-689
    • Brändén, C.I.1    Jones, T.A.2
  • 2
    • 0029644940 scopus 로고
    • Where freedom is given, liberties are taken
    • Kleywegt, G. J. and Jones, T. A. (1995) Where freedom is given, liberties are taken. Structure 3, 535-540.
    • (1995) Structure , vol.3 , pp. 535-540
    • Kleywegt, G.J.1    Jones, T.A.2
  • 3
    • 0034013435 scopus 로고    scopus 로고
    • Validation of protein crystal structures
    • Kleywegt, G. J. (2000) Validation of protein crystal structures. Acta Crystallogr. D56, 249-265.
    • (2000) Acta Crystallogr , vol.D56 , pp. 249-265
    • Kleywegt, G.J.1
  • 4
    • 0038336897 scopus 로고    scopus 로고
    • Application and limitations of X-ray crystallographic data in structure-based ligand and drug design
    • Davis, A. M., Teague, S. J., and Kleywegt, G. J. (2003) Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew. Chem. Int. Ed. 42, 2718-2736.
    • (2003) Angew. Chem. Int. Ed , vol.42 , pp. 2718-2736
    • Davis, A.M.1    Teague, S.J.2    Kleywegt, G.J.3
  • 5
    • 0041333142 scopus 로고    scopus 로고
    • Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?
    • Kleywegt, G. J., Henrick, K., Dodson, E. J., and van Aalten, D. M. F. (2003) Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement? Structure 11, 1051-1059.
    • (2003) Structure , vol.11 , pp. 1051-1059
    • Kleywegt, G.J.1    Henrick, K.2    Dodson, E.J.3    van Aalten, D.M.F.4
  • 6
    • 36549014038 scopus 로고    scopus 로고
    • Retrieval and validation of structural information
    • Sundström, M, Norin, M, and Edwards, A, eds, Taylor and Francis, Boca Raton, FL, pp
    • Kleywegt, G. J. and Hansson, H. (2005) Retrieval and validation of structural information. In: Structural Genomics and High Throughput Structural Biology (Sundström, M., Norin, M., and Edwards, A., eds.), Taylor and Francis, Boca Raton, FL, pp. 185-222.
    • (2005) Structural Genomics and High Throughput Structural Biology , pp. 185-222
    • Kleywegt, G.J.1    Hansson, H.2
  • 7
    • 0027999315 scopus 로고
    • Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy
    • MacArthur, M. W., Laskowski, R. A., and Thornton, J. M. (1994) Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr. Opin. Struct. Biol. 4, 731-737.
    • (1994) Curr. Opin. Struct. Biol , vol.4 , pp. 731-737
    • MacArthur, M.W.1    Laskowski, R.A.2    Thornton, J.M.3
  • 8
    • 0028039323 scopus 로고
    • An evaluation of the use of databases in protein structure refinement
    • Zou, J. Y. and Mowbray, S. L. (1994) An evaluation of the use of databases in protein structure refinement. Acta Crystallogr. D50, 237-249.
    • (1994) Acta Crystallogr , vol.D50 , pp. 237-249
    • Zou, J.Y.1    Mowbray, S.L.2
  • 9
    • 0008840364 scopus 로고
    • Braille for pugilists
    • Hunter, W. N, Thornton, J. M, and Bailey, S, eds, SERC Daresbury Laboratory, Warrington, UK, pp
    • Kleywegt, G. J. and Jones, T. A. (1995) Braille for pugilists. In: Making the Most of Your Model, (Hunter, W. N., Thornton, J. M., and Bailey, S., eds.), SERC Daresbury Laboratory, Warrington, UK, pp. 11-24.
    • (1995) Making the Most of Your Model , pp. 11-24
    • Kleywegt, G.J.1    Jones, T.A.2
  • 10
    • 0039299578 scopus 로고    scopus 로고
    • EU 3-D Validation Network (1998) Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J. Mol. Biol. 276, 417-436.
    • EU 3-D Validation Network (1998) Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J. Mol. Biol. 276, 417-436.
  • 12
    • 0037263939 scopus 로고    scopus 로고
    • Structural quality assurance
    • Bourne, P. E. and Weissig, H, eds, Wiley-Liss, Hoboken, NJ, pp
    • Laskowski, R. A. (2003) Structural quality assurance. In: Structural Bioinformatics, (Bourne, P. E. and Weissig, H., eds.), Wiley-Liss, Hoboken, NJ, pp. 273-303.
    • (2003) Structural Bioinformatics , pp. 273-303
    • Laskowski, R.A.1
  • 13
    • 0017411710 scopus 로고
    • The Protein Data Bank: A computer-based archival file for macromolecular structures
    • Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., et al. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
    • (1977) J. Mol. Biol , vol.112 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3
  • 15
    • 0028103275 scopus 로고    scopus 로고
    • Collaborative Computational Project, Nr. 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760-763.
    • Collaborative Computational Project, Nr. 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760-763.
  • 17
    • 0030498233 scopus 로고    scopus 로고
    • xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electrondensity maps and reflection data sets
    • Kleywegt, G. J. and Jones, T. A. (1996) xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electrondensity maps and reflection data sets. Acta Crystallogr. D52, 826-828.
    • (1996) Acta Crystallogr , vol.D52 , pp. 826-828
    • Kleywegt, G.J.1    Jones, T.A.2
  • 18
    • 0030497978 scopus 로고    scopus 로고
    • Efficient rebuilding of protein structures
    • Kleywegt, G. J. and Jones, T. A. (1996) Efficient rebuilding of protein structures. Acta Crystallogr. D52, 829-832.
    • (1996) Acta Crystallogr , vol.D52 , pp. 829-832
    • Kleywegt, G.J.1    Jones, T.A.2
  • 19
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110-119.
    • (1991) Acta Crystallogr , vol.A47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 20
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240-255.
    • (1997) Acta Crystallogr , vol.D53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 21
  • 22
    • 84944812409 scopus 로고
    • Improved Fourier coefficients for maps using phases from partial structures with errors
    • Read, R. J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140-149.
    • (1986) Acta Crystallogr , vol.A42 , pp. 140-149
    • Read, R.J.1
  • 24
    • 0031574325 scopus 로고    scopus 로고
    • Not your average density
    • Kleywegt, G. J. and Read, R. J. (1997) Not your average density. Structure 5, 1557-1569.
    • (1997) Structure , vol.5 , pp. 1557-1569
    • Kleywegt, G.J.1    Read, R.J.2
  • 25
    • 0000268861 scopus 로고
    • Calculation of an OMIT map
    • Bhat, T. N. (1988) Calculation of an OMIT map. J. Appl. Crystallogr. 21, 279-281.
    • (1988) J. Appl. Crystallogr , vol.21 , pp. 279-281
    • Bhat, T.N.1
  • 26
    • 84945096204 scopus 로고
    • Model bias in macromolecular crystal structures
    • Hodel, A., Kim, S. H., and Brünger, A. T. (1992) Model bias in macromolecular crystal structures. Acta Crystallogr. A48, 851-858.
    • (1992) Acta Crystallogr , vol.A48 , pp. 851-858
    • Hodel, A.1    Kim, S.H.2    Brünger, A.T.3
  • 27
    • 0001408294 scopus 로고    scopus 로고
    • Computation of Bhat's OMIT map with different coefficients
    • Vellieux, F. M. D. and Dijkstra, B. W (1997) Computation of Bhat's OMIT map with different coefficients. J. Appl. Crystallogr. 30, 396-399.
    • (1997) J. Appl. Crystallogr , vol.30 , pp. 396-399
    • Vellieux, F.M.D.1    Dijkstra, B.W.2
  • 28
    • 0027542118 scopus 로고
    • Quality control of protein models: Directional atomic contact analysis
    • Vriend, G. and Sander, C. (1993) Quality control of protein models: directional atomic contact analysis. J. Appl. Crystallogr. 26, 47-60.
    • (1993) J. Appl. Crystallogr , vol.26 , pp. 47-60
    • Vriend, G.1    Sander, C.2
  • 29
    • 2542554197 scopus 로고    scopus 로고
    • Verification of protein structures: Side-chain planarity
    • Hooft, R. W W., Sander, C., and Vriend, G. (1996) Verification of protein structures: side-chain planarity. J. Appl. Crystallogr. 29, 714-716.
    • (1996) J. Appl. Crystallogr , vol.29 , pp. 714-716
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 30
    • 0030870075 scopus 로고    scopus 로고
    • Objectively judging the quality of a protein structure from a Ramachandran plot
    • Hooft, R. W. W., Sander, C. and Vriend, G. (1997) Objectively judging the quality of a protein structure from a Ramachandran plot. Comput. Applic. Biosci. 13, 425-430.
    • (1997) Comput. Applic. Biosci , vol.13 , pp. 425-430
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 31
    • 0032215320 scopus 로고    scopus 로고
    • Databases in protein crystallography
    • Kleywegt, G. J. and Jones, T. A. (1998) Databases in protein crystallography. Acta Crystallogr. D54, 1119-1131.
    • (1998) Acta Crystallogr , vol.D54 , pp. 1119-1131
    • Kleywegt, G.J.1    Jones, T.A.2
  • 32
    • 0030841587 scopus 로고    scopus 로고
    • Electron density map interpretation
    • Jones, T. A. and Kjeldgaard, M. (1997) Electron density map interpretation. Methods Enzymol. 277, 173-208.
    • (1997) Methods Enzymol , vol.277 , pp. 173-208
    • Jones, T.A.1    Kjeldgaard, M.2
  • 33
    • 0030845843 scopus 로고    scopus 로고
    • Model-building and refinement practice
    • Kleywegt, G. J. and Jones, T. A. (1997) Model-building and refinement practice. Methods Enzymol. 277, 208-230.
    • (1997) Methods Enzymol , vol.277 , pp. 208-230
    • Kleywegt, G.J.1    Jones, T.A.2
  • 34
    • 0026597444 scopus 로고
    • Free R value: A novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger, A. T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475.
    • (1992) Nature , vol.355 , pp. 472-475
    • Brünger, A.T.1
  • 35
    • 0030586823 scopus 로고    scopus 로고
    • Checking your imagination: Applications of the free R value
    • Kleywegt, G. J. and Brünger, A. T. (1996) Checking your imagination: applications of the free R value. Structure 4, 897-904.
    • (1996) Structure , vol.4 , pp. 897-904
    • Kleywegt, G.J.1    Brünger, A.T.2
  • 36
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
    • (1993) J. Appl. Crystallogr , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 37
    • 0030589514 scopus 로고    scopus 로고
    • Phi/Psi-chology: Ramachandran revisited
    • Kleywegt, G. J. and Jones, T. A. (1996) Phi/Psi-chology: Ramachandran revisited. Structure 4, 1395-1400.
    • (1996) Structure , vol.4 , pp. 1395-1400
    • Kleywegt, G.J.1    Jones, T.A.2
  • 39
    • 0030767485 scopus 로고    scopus 로고
    • VERIFY3D: Assessment of protein models with three-dimensional profiles
    • Eisenberg, D., Lüthy, R., and Bowie, J. U. (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 211, 396-404.
    • (1997) Methods Enzymol , vol.211 , pp. 396-404
    • Eisenberg, D.1    Lüthy, R.2    Bowie, J.U.3
  • 40
    • 36549068623 scopus 로고    scopus 로고
    • Dym, O., Eisenberg, D., and Yeates, T. O. (2001) Detection of errors in protein models. In: International Tables for Crystallography. F. Crystallography of Biological Macromolecules (Rossmann, M.G. and Arnold, E., eds.), Kluwer, Dordrecht, The Netherlands, pp. 520-525.
    • Dym, O., Eisenberg, D., and Yeates, T. O. (2001) Detection of errors in protein models. In: International Tables for Crystallography. Volume F. Crystallography of Biological Macromolecules (Rossmann, M.G. and Arnold, E., eds.), Kluwer, Dordrecht, The Netherlands, pp. 520-525.
  • 41
    • 0030501419 scopus 로고    scopus 로고
    • Use of non-crystallographic symmetry in protein structure refinement
    • Kleywegt, G. J. (1996) Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D52, 842-857.
    • (1996) Acta Crystallogr , vol.D52 , pp. 842-857
    • Kleywegt, G.J.1
  • 42
    • 0033229975 scopus 로고    scopus 로고
    • Experimental assessment of differences between related protein crystal structures
    • Kleywegt, G. J. (1999) Experimental assessment of differences between related protein crystal structures. Acta Crystallogr. D55, 1878-1884.
    • (1999) Acta Crystallogr , vol.D55 , pp. 1878-1884
    • Kleywegt, G.J.1
  • 43
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structure refinement
    • Engh, R. A. and Huber, R. (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A47, 392-400.
    • (1991) Acta Crystallogr , vol.A47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 45
    • 36549052074 scopus 로고    scopus 로고
    • Engh, R. A. and Huber, R. (2001) Structure quality and target parameters, in International Tables for Crystallography. F Crystallography of Biological Macromolecules, (Rossmann, M. G., and Arnold, E., eds.), Kluwer, Dordrecht, The Netherlands, pp. 382-392.
    • Engh, R. A. and Huber, R. (2001) Structure quality and target parameters, in International Tables for Crystallography. Volume F Crystallography of Biological Macromolecules, (Rossmann, M. G., and Arnold, E., eds.), Kluwer, Dordrecht, The Netherlands, pp. 382-392.
  • 47
    • 0023140814 scopus 로고
    • Crystallographic R factor refinement by molecular dynamics
    • Brünger, A. T., Kuriyan, J., and Karplus, M. (1987) Crystallographic R factor refinement by molecular dynamics. Science 235, 458-460.
    • (1987) Science , vol.235 , pp. 458-460
    • Brünger, A.T.1    Kuriyan, J.2    Karplus, M.3
  • 48
    • 3543012707 scopus 로고    scopus 로고
    • Crystallography and NMR System: A new software suite for macromolecular structure determination
    • Brünger, A. T., Adams, P. D., Clore, G. M., et al. (1998) Crystallography and NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr. D54, 905-921.
    • (1998) Acta Crystallogr , vol.D54 , pp. 905-921
    • Brünger, A.T.1    Adams, P.D.2    Clore, G.M.3
  • 49
    • 0030757720 scopus 로고    scopus 로고
    • The TNT refinement package
    • Tronrud, D. E. (1997) The TNT refinement package. Methods Enzymol. 277, 306-319.
    • (1997) Methods Enzymol , vol.277 , pp. 306-319
    • Tronrud, D.E.1
  • 50
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density
    • McRee, D. E. (1999) XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156-165.
    • (1999) J. Struct. Biol , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 51
    • 0030880598 scopus 로고    scopus 로고
    • SHELXL: High-resolution refinement
    • Sheldrick, G. M. and Schneider, T. R. (1997) SHELXL: high-resolution refinement. Methods Enzymol. 211, 319-344.
    • (1997) Methods Enzymol , vol.211 , pp. 319-344
    • Sheldrick, G.M.1    Schneider, T.R.2
  • 52
    • 0032896079 scopus 로고    scopus 로고
    • Difference density quality (DDQ): A method to assess the global and local correctness of macromolecular crystal structures
    • Van den Akker, F. and Hol, W G. J. (1999) Difference density quality (DDQ): a method to assess the global and local correctness of macromolecular crystal structures. Acta Crystallogr. D55, 206-218.
    • (1999) Acta Crystallogr , vol.D55 , pp. 206-218
    • Van den Akker, F.1    Hol, W.G.J.2
  • 53
    • 0027180507 scopus 로고
    • Verification of protein structures: Patterns of nonbonded atomic interactions
    • Colovos, C. and Yeates, T. O. (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Prot. Sci. 2, 1511-1519.
    • (1993) Prot. Sci , vol.2 , pp. 1511-1519
    • Colovos, C.1    Yeates, T.O.2
  • 54
    • 36549065103 scopus 로고    scopus 로고
    • Kleywegt, G. J., Zou, J. Y., Kjeldgaard, M., and Jones, T. A. (2002) Around O. International Tables for Crystallography, F, Crystallography of Biological Macromolecules (Rossmann, M. G. and Arnold, E., eds.), Kluwer, Dordrecht, The Netherlands, pp. 353-367.
    • Kleywegt, G. J., Zou, J. Y., Kjeldgaard, M., and Jones, T. A. (2002) Around O. International Tables for Crystallography, Volume F, Crystallography of Biological Macromolecules (Rossmann, M. G. and Arnold, E., eds.), Kluwer, Dordrecht, The Netherlands, pp. 353-367.
  • 55
    • 0034989056 scopus 로고    scopus 로고
    • Checking nucleic acid crystal structures
    • Das, U., Chen, S., Fuxreiter, M., et al. (2001) Checking nucleic acid crystal structures. Acta Crystallogr. D57, 813-828.
    • (2001) Acta Crystallogr , vol.D57 , pp. 813-828
    • Das, U.1    Chen, S.2    Fuxreiter, M.3
  • 56
    • 0000356656 scopus 로고
    • A graphics model building and refinement system for macromolecules
    • Jones, T. A. (1978) A graphics model building and refinement system for macromolecules. J. Appl. Crystallogr. 11, 268-272.
    • (1978) J. Appl. Crystallogr , vol.11 , pp. 268-272
    • Jones, T.A.1
  • 57
    • 0035177219 scopus 로고    scopus 로고
    • A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent
    • Oldfield, T. J. (2001) A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent. Acta Crystallogr. D57, 82-94.
    • (2001) Acta Crystallogr , vol.D57 , pp. 82-94
    • Oldfield, T.J.1
  • 58
    • 0032922193 scopus 로고    scopus 로고
    • SFCHECK: A unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model
    • Vaguine, A. A., Richelle, J., and Wodak, S. J. (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr. D55, 191-205.
    • (1999) Acta Crystallogr , vol.D55 , pp. 191-205
    • Vaguine, A.A.1    Richelle, J.2    Wodak, S.J.3
  • 59
    • 0030484164 scopus 로고    scopus 로고
    • Towards the automatic interpretation of macromolecular electron-density maps: Qualitative and quantitative matching of protein sequence to map
    • Zou, J. Y. and Jones, T. A. (1996) Towards the automatic interpretation of macromolecular electron-density maps: qualitative and quantitative matching of protein sequence to map. Acta Crystallogr. D52, 833-841.
    • (1996) Acta Crystallogr , vol.D52 , pp. 833-841
    • Zou, J.Y.1    Jones, T.A.2
  • 60
    • 0002701773 scopus 로고
    • Crystallographic refinement of macromolecules having non-crystallographic symmetry
    • Jones, T. A. and Liljas, L. (1984) Crystallographic refinement of macromolecules having non-crystallographic symmetry. Acta Crystallogr. A40, 50-57.
    • (1984) Acta Crystallogr , vol.A40 , pp. 50-57
    • Jones, T.A.1    Liljas, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.