Page 123 - Macromolecular Crystallography
P. 123

112  MACROMOLECULAR CRYS TALLOGRAPHY

        Bentley, G. (1997) Phased translation function. Method  Delarue, M. and Sanejouand, Y. H. (2002) Simplified
          Enzymol. 276, 611–619.                      normal mode analysis of conformational transitions
        Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G.,  in DNA-dependent polymerases: the elastic network
          Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne,  model. J. Mol. Biol. 320, 1011–1024.
          P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28,  Delarue, M., Boule, J. B., Lescar, J., Expert-Bezancon, N.,
          235–242.                                    Jourdan,  N.,  Sukumar,  N.,  Rougeon,  F.,  and
        Brünger, A. T. (1997) Free R values: Cross-validation in  Papanicolaou,  C. (2002) Crystal structures of a
          crystallography. Method Enzymol. 277, 366–396.  template-independent DNA polymerase: murine termi-
        Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L.,  nal deoxynucleotidyltransferase. EMBO J. 21, 427–439.
          Gros, P., Grosse-Kunstleve, R. W., et al. (1998) Crystallog-  Delarue, M. and Dumas, P. (2004) On the use of low-
          raphy and NMR system: Anew software suite for macro-  frequency normal modes to enforce collective move-
          molecular structure determination. Acta Crystallogr. D  ments in refining macromolecular structural models.
          54, 905–921.                                Proc. Natl. Acad. Sci. USA 101, 6957–6962.
        Burling, F. T. and Brünger, A. T. (1994) Thermal motion and  Delarue, M., Duclert-Savatier, N., Miclet, E., Haouz, A.,
          conformational disorder in protein crystal structures. Isr.  Giganti, D., Ouazzani, J., Lopez, P. Nilges, M.
          J. Chem. 34, 165–175.                       and Stoven, V. (2007) Three dimensional structure
        CASP5 (2003). Proteins, 53, Suppl. 6.         and implications for the catalytic mechanism of
        Catherinot, V. and Labesse, G. (2004) ViTO: tool for  6-phosphogluconolactonase from Trypanosoma brucei.
          refinement of protein sequence-structure alignments.  J. Mol. Biol. 366, 868–881.
          Bioinformatics, 20: 3694–3696.             Douguet, M. and Labesse, G. (2001) Easier threading
        Chang, G. and Lewis, M. (1997) Molecular replace-  through web-based comparisons and cross-validations.
          ment using genetic algorithms. Acta Crystallogr. D 53,  Bioinformatics 17, 752–753.
          279–289.                                   Fokine, A. and Urzhumtsev, A. (2002) On the use of
        Chen, Y. W. (2001) Solution solution: using NMR models  low-resolution data for translation search in molecular
          for molecular replacement. Acta Crystallogr. D 57,  replacement. Acta Crystallogr. D 58, 72–74.
          1457–1461.                                 Glykos, N. M. and Kokkinidis, M. (2000) A stochastic
        Chothia, C. and Lesk, A. (1986) The relation between  approach to molecular replacement. Acta Crystallogr. D
          the divergence of sequence and structure in proteins.  56, 169–174.
          EMBO J. 5, 823–826.                        Glykos, N.M.andKokkinidis, M.(2001)Multi-dimensional
        Claude, J. B., Suhre, K., Notredame, C., Claverie, J. M.,  molecular replacement. Acta Crystallogr. D 57, 1462–
          and Abergel, C. (2004) CaspR: a web server for auto-  1473.
          mated molecular replacement using homology mod-  Glykos, N. M. and Kokkinidis, M. (2003) Structure deter-
          elling. Nucleic Acids Res. 32, W606–609.    mination of a small protein through a 23-dimensional
        Collaborative Computational Project (1994) The CCP4  molecular-replacement search. Acta Crystallogr. D 59,
          suite: programs for protein crystallography. Acta Crys-  709–718.
          tallogr. D 50, 760–763.                    Harada, Y., Lifchitz, A., Berthou, J., and Jolles, P. (1981)
        Crowther, R. A. (1972). The fast rotation function. In: The  A translation function combining packing and diffrac-
          Molecular Replacement Method, Rossmann, M. G., ed.  tion information: an application to lysozyme (high-
          Gordon and Breach, New York, pp. 173–185.   temperature form). Acta Crystallogr. A 37, 398–406.
        Crowther, R. A. and Blow, D. M. (1967) A method of  Huber, R. and Schneider, M. (1985) A group refine-
          positioning a known molecule in an unknown crystal  ment procedure in protein crystallography using Fourier
          structure. Acta Crystallogr. 23, 544–548.   transforms. J. Appl. Crystallogr. 18, 165–169.
        DeLano, W. L. and Brünger, A. T. (1995) The direct  Jamrog, D. C., Zhang, Y., and Phillips, G. N., Jr. (2003)
          rotation function: Patterson correlation search applied  SOMoRe: a multi-dimensional search and optimization
          to molecular replacement. Acta Crystallogr. D 51,  approach to molecular replacement. Acta Crystallogr. D
          740–748.                                    59, 304–314.
        Delarue, M., Samama, J. P., Mourey, L., and Moras, D.  Jamrog, D. C., Zhang, Y., and Phillips, G. N., Jr. (2004) On
          (1990) Crystal structure of bovine antithrombin III. Acta  the equivalence between a commonly used correlation
          Crystallogr. B 46, 550–556.                 coefficient and a least-squares function. Acta Crystallogr.
        Delarue, M. and Orland, H. (2000). General formalism  A 60, 214–219.
          for phase combination and phase refinement: a statis-  Jones, D. T. (2001) Evaluating the potential of using fold-
          tical thermodynamics approach in reciprocal space. Acta  recognition models for molecular replacement. Acta
          Crystallogr. A 56, 562–574.                 Crystallogr. D 57, 1428–1434.
   118   119   120   121   122   123   124   125   126   127   128