Page 124 - Macromolecular Crystallography

MOLECULAR REPLACEMENT TECHNIQUES 113

Jones, T. A., Zhou, J. Y., Cowan, S. W., and Kjelgaard, M. Notredame, C., Higgins, D., and Heringa, J. (2000) T-
(1991) Improved methods for building protein models in Coffee: A novel method for fast and accurate multiple
electron density maps and the location of errors in these sequence alignment. J. Mol. Biol. 302, 205–217.
models. Acta Crystallogr. A 47, 110–119. O’Sullivan, O., Suhre, K., Abergel, C., Higgins, D. G.,
Keegan, R. M. and Wynn, M. D. (2007) Automated search- and Notredame, C. (2004) 3DCoffee: combining pro-
model discovery and preparation for structure solu- tein sequences and structures within multiple sequence
tion by molecular replacement. Acta Crystallogr. D 63, alignment. J. Mol. Biol. 340, 385–395.
447–457. Pellegrini, M., Gronbech-Jensen, N., Kelly, J.A., Pfluegl, G.,
Kissinger, C. R., Gelhaar, D. K., and Fogel, D. B. (1999) and Yeates, T. O. (1997) Highly constrained multiple-
Rapid automated molecular replacement by evolution- copy refinement of protein crystal structures. Proteins 29,
ary search. Acta Crystallogr. D 55, 484–491. 426–432.
Kissinger, C. R., Gelhaar, D. K., Smith, B. A., and Perrakis,A., Harkiolaki, M., Wilson, K. S., and Lamzin, V. S.
Bouzida, D. (2001) Molecular replacement by evolution- (2001) ARP/wARP and molecular replacement. Acta
ary search. Acta Crystallogr. D 57, 1474–1479. Crystallogr. D 57, 1445–1450.
Koehl, P. and Delarue, M. (1994) Application of a self- Rao, S. N., Hih, J. H., and Hartsuck, J. A. (1980)
consistent mean field theory to predict protein side- Rotation-function space groups. Acta Crystallogr. A 36,
chains conformation and estimate their conformational 878–884.
entropy. J. Mol. Biol. 239, 249–275. Read, R. J. (1986) Improved Fourier coefficients for maps
Koehl, P. and Delarue, M. (1995) A self consistent mean using phases from partial structures with errors. Acta
field approach to simultaneous gap closure and side- Crystallogr. A 42, 140–149.
chain positioning in homology modelling. Nature Struct. Read, R. J. (1990) Structure-factor probabilities for related
Biol. 2, 163–170. structures. Acta Crystallogr. A 46, 900–912.
Krebs, W. G., Alexandrov, V., Wilson, C. A., Echols, N, Read, R. J. (2001) Pushing the boundaries of molecular
Yu, H., and Gerstein, M. (2002) Normal mode analysis replacement with maximum likelihood. Acta Crystallogr.
of macromolecular motions in a database framework: D 57, 1373–1382.
developing mode concentration as a useful classifying Rossmann, M. G. (1990) The molecular replacement
statistic. Proteins 48, 682–695. method. Acta Crystallogr. A 46, 73–82.
Lee, S., Sawaya, M. R., and Eisenberg, D. (2003) Structure Rossmann, M. G. and Blow, D. M. (1962) The detection of
of superoxide dismutase from Pyrobaculum aerophilum sub-units within the crystallographic asymmetric unit.
presents a challenging case in molecular replacement Acta Crystallogr. 15, 24–31.
with multiple molecules, pseudo-symmetry and twin- Rupp, B., Segelke, B.W., Krupka, H.I., Lekin, T.,
ning. Acta Crystallogr. D 59, 2191–2199. Shafer, J., Zemla, A., Topani, D., Snell, G., and
Li de la Sierra, I., Munier-Lehmann, H., Gilles, A. M., Earnest, G. (2002).The TB structural genomics consor-
Barzu, O., and Delarue, M. (2001) X-ray structure of tium crystallization facility: towards automation from
TMP kinase from Mycobacterium tuberculosis complexed protein to electron density. Acta Crystallogr. D 58,
with TMP at 1.95 A resolution. J. Mol. Biol. 311, 1514–1518.
87–100. Sali, A. and Blundell, T. L. (1993) Comparative protein
Lindahl, E., Azuara, C., Koehl, P. and Delarue, M. (2006) modelling by satisfaction of spatial restraints. J. Mol. Biol.
NOMAD-Ref: visualization, deformation and refine- 234, 779–815.
ment of macromolecular structures based on all-atom Schwarzenbacher, R., Godzik, A., Grzechnik, S. K., and
normal mode analysis. Nucleic Acid Res. 34, W52–56. Jaroszewski, L. (2004) The importance of alignment accu-
Murshudov, G. N., Vagin, A. A., and Dodson, E. J. racy for molecular replacement. Acta Crystallogr. D 60,
(1997) Refinement of macromolecular structures by the 1229–1236.
maximum-likelihood method. Acta Crystallogr. D 53, Sheriff, S., Klei, H. E., and Davis, M. E. (1999) Imple-
240–255. mentation of a six-dimensional search using the AMoRe
Navaza, J. (2001) Implementation of molecular replace- translation function for difficult molecular-replacement
ment in AmoRe. Acta Crystallogr. D 57, 1367–1372. problems. J. Appl. Crystallogr. 32, 98–101.
Navaza, J. (2001). Rotation functions. In: International Tables Storoni, L. C., McCoy, A. J., and Read, R. J. (2004)
of Crystallography, vol. F, p. 269–274. KluwerAcademic Likelihood-enhanced fast rotation functions. Acta
Publishers. Dordrecht, Boston, London. Crystallogr. D 60, 432–438.
Navaza, J. and Saludjian, P. (1997) AmoRe: an automated Stubbs, M. T. and Huber, R. (1991) An analytical packing
molecular replacement package. Method Enzymol. 276, function employing Fourier transforms. Acta Crystallogr.
581–594. A 47, 521–526.