Access the full text.
Sign up today, get DeepDyve free for 14 days.
V. Lunin, M. Woolfson (1993)
Mean phase error and the map-correlation coefficient.Acta crystallographica. Section D, Biological crystallography, 49 Pt 6
A. Pautsch, G. Schulz (1998)
Structure of the outer membrane protein A transmembrane domainNature Structural Biology, 5
D. Raimondo, A. Giorgetti, S. Bosi, A. Tramontano (2006)
Automatic procedure for using models of proteins in molecular replacementProteins: Structure, 66
Jiangdi Fan, Ding Wei (2010)
Improvement of a new rotation function for molecular replacement by designing new scoring functions and dynamic correlation coefficientChinese Physics B, 19
C. Kissinger, D. Gehlhaar, Barry Smith, D. Bouzida (2001)
Molecular replacement by evolutionary search.Acta crystallographica. Section D, Biological crystallography, 57 Pt 10
M. Rossmann (1990)
The molecular replacement method.Acta crystallographica. Section A, Foundations of crystallography, 46 ( Pt 2)
M. Petoukhov, D. Svergun (2007)
Analysis of X-ray and neutron scattering from biomacromolecular solutions.Current opinion in structural biology, 17 5
S. Brenner, P. Koehl, M. Levitt (2000)
The ASTRAL compendium for protein structure and sequence analysisNucleic acids research, 28 1
Collaborative Computational (1994)
The CCP4 suite: programs for protein crystallography.Acta crystallographica. Section D, Biological crystallography, 50 Pt 5
T. Ueno, T. Koshiyama, M. Ohashi, K. Kondo, Masaharu Kono, A. Suzuki, T. Yamane, Y. Watanabe (2005)
Coordinated design of cofactor and active site structures in development of new protein catalysts.Journal of the American Chemical Society, 127 18
James Casbon, G. Crooks, M. Saqi (2006)
A high level interface to SCOP and ASTRAL implemented in PythonBMC Bioinformatics, 7
W. Press, S. Teukolsky, W. Vetterling, B. Flannery (2002)
Numerical recipes in C
Jack Schonbrun, W. Wedemeyer, D. Baker (2002)
Protein structure prediction in 2002.Current opinion in structural biology, 12 3
F. Jiang, Z. Rao (2001)
A new implementation of the molecular replacement method using a six-dimensional Patterson vector search.Journal of synchrotron radiation, 8 3
(1990)
Acta Cryst
F. Jiang (2008)
A new rotation function for molecular replacement by using both the self and cross Patterson vectors.Acta crystallographica. Section D, Biological crystallography, 64 Pt 5
W. Delano, A. Brunger (1995)
The direct rotation function: rotational Patterson correlation search applied to molecular replacementActa Crystallographica Section D-biological Crystallography, 51
R. Grosse-Kunstleve, Paul Adams (2001)
Patterson correlation methods: a review of molecular replacement with CNS.Acta crystallographica. Section D, Biological crystallography, 57 Pt 10
D. Rigden, R. Keegan, M. Winn (2008)
Molecular replacement using ab initio polyalanine models generated with ROSETTA.Acta crystallographica. Section D, Biological crystallography, 64 Pt 12
C. Bystroff, Y. Shao (2002)
Fully automated ab initio protein structure prediction using I-STES, HMMSTR and ROSETTABioinformatics, 18 Suppl 1
(2006)
BMC Bioinformatics , 7 , 10 . Collaborative Computational Project , Number 4 ( 1994 )
A new real‐space implementation of the molecular‐replacement method is described. The method locates the search model in the target crystal by maximizing the matching between the search‐model vectors and the Patterson self and cross vectors. In previous work, a new rotation function was introduced for the molecular‐replacement method [Jiang (2008). Acta Cryst. D64, 561–566]. This rotation function is calculated by matching the search model directly with both the Patterson self and cross vectors in real space. All the matches are summed and averaged to enhance the overall signal‐to‐noise ratio for a given orientation of the search model. Recently, to avoid the dependence of the weights derived from the linear regression on the properties of the search model and the target crystal structure, such as secondary structures, space groups and cell parameters, a dynamic correlation coefficient has been designed and used as the total rotation function score [Jiang & Ding (2010). Chin. Phys. B, 19, 106101]. This work further extends this idea to the implementation of translation search. A new real‐ or direct‐space translation function has been implemented by matching the cross vectors between the symmetry mates of the search model to the Patterson cross vectors. This method enables effective searching for small helix fragments in the target crystal. Although the solution model assembled by using multiple fragments of helix is insufficient to start ab initio phasing of the target crystal, it can be used to identify the known protein folds in the Protein Data Bank that are homologous to the target structure. It can also be combined with other experimental and theoretical models to screen and select for better search models for molecular replacement.
Acta Crystallographica Section A Foundations of Crystallography – Wiley
Published: Jan 1, 2011
Keywords: ; ; ;
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.