Acta Crystallographica Section D

Biological Crystallography

Volume 57, Part 10 (October 2001)


Molecular replacement and its relatives

Proceedings of the CCP4 study weekend

[Buy print version] A printed copy of this issue is available for purchase

[Preface]
[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Molecular shape of AxNiR obtained directly from solution scattering and located in the unit cell by using the FSEARCH program (p. 1410). Dr J. G. Grossmann is thanked for the help with the figures.

research papers


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Acta Cryst. (2001). D57, 1355-1359  [ doi:10.1107/S0907444901012410 ]

Rotations and rotation matrices

P. R. Evans

Synopsis: A discussion of the elementary properties of rotation matrices and their represention as polar or Eulerian angles.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1360-1366  [ doi:10.1107/S0907444901009386 ]

Molecular replacement - historical background

M. G. Rossmann

Synopsis: A review is given of the mathematical procedures required for a molecular-replacement structure determination.

Online 21 September 2001


 

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Acta Cryst. (2001). D57, 1367-1372  [ doi:10.1107/S0907444901012422 ]

Implementation of molecular replacement in AMoRe

J. Navaza

Synopsis: An account is given of the molecular replacement method as implemented in the package AMoRe.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1373-1382  [ doi:10.1107/S0907444901012471 ]

Pushing the boundaries of molecular replacement with maximum likelihood

R. J. Read

Synopsis: The use of likelihood, particularly a multivariate likelihood function for multiple molecular-replacement models, allows difficult molecular-replacement problems to be solved more easily.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1383-1389  [ doi:10.1107/S0907444901012446 ]

How to take advantage of non-crystallographic symmetry in molecular replacement: `locked' rotation and translation functions

L. Tong

Synopsis: The locked rotation and translation functions are a powerful way of taking advantage of the presence of non-crystallographic symmetry in a structure determination by the molecular-replacement method.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1390-1396  [ doi:10.1107/S090744490101246X ]

Patterson correlation methods: a review of molecular replacement with CNS

R. W. Grosse-Kunstleve and P. D. Adams

Synopsis: The principles and the implementation of the molecular-replacement procedures in CNS are reviewed.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1397-1404  [ doi:10.1107/S0907444901012434 ]

NMR trial models: experiences with the colicin immunity protein Im7 and the p85[alpha] C-terminal SH2-peptide complex

R. A. Pauptit, C. A. Dennis, D. J. Derbyshire, A. L. Breeze, S. A. Weston, S. Rowsell and G. N. Murshudov

Synopsis: Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the E. coli colicin immunity protein Im7; the other is the previously unreported crystal structure of the carboxy-terminal SH2 domain from the p85[alpha] subunit of human phosphatidylinositol 3-OH kinase complexed to a PDGF receptor-derived specificity peptide.

PDB references: 1h9o and 1ayi

Online 21 September 2001


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Acta Cryst. (2001). D57, 1405-1409  [ doi:10.1107/S0907444901013415 ]

Using electron-microscopy images as a model for molecular replacement

E. J. Dodson

Synopsis: This review summarizes the steps required to exploit electron-microscopy images as models for molecular replacement, indicating some of the associated practical problems.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1410-1414  [ doi:10.1107/S0907444901009374 ]

Phasing from an envelope

Q. Hao

Synopsis: The program FSEARCH can be used for a molecular-replacement solution, given a predetermined envelope from any source, such as solution scattering.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1415-1420  [ doi:10.1107/S0907444901009829 ]

Molecular placement of experimental electron density: a case study on UDP-galactopyranose mutase

D. A. R. Sanders, S. A. McMahon, G. L. Leonard and J. H. Naismith

Synopsis: The paper describes the structure solution of UDP-galactopyranomutase. The structure solution relied on the placement of experimental density into a new crystal form.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1421-1427  [ doi:10.1107/S0907444901012483 ]

Creating structure features by data mining the PDB to use as molecular-replacement models

T. J. Oldfield

Synopsis: Mathematical data mining is used to generate a representative set of protein fragments to use as search models in molecular replacement.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1428-1434  [ doi:10.1107/S0907444901013403 ]

Evaluating the potential of using fold-recognition models for molecular replacement

D. T. Jones

Synopsis: The proposal is investigated that protein tertiary structure prediction methods and threading methods in particular might be applied to the problem of solving a protein structure by X-ray crystallography.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1435-1444  [ doi:10.1107/S0907444901010812 ]

Fast Fourier feature recognition

K. Cowtan

Synopsis: Fast Fourier feature recognition is one approach to the automatic identification of protein-like features from crystallographic data. This approach has been implemented in a computationally efficient manner and refined to work with inferior data.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1445-1450  [ doi:10.1107/S0907444901014007 ]

ARP/wARP and molecular replacement

A. Perrakis, M. Harkiolaki, K. S. Wilson and V. S. Lamzin

Synopsis: The capabilities of the ARP/wARP software for refining and automatically building protein models, starting from molecular-replacement solutions, are presented. Useful protocols are suggested based on worked examples.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1451-1456  [ doi:10.1107/S0907444901012409 ]

Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps

A. A. Vagin and M. N. Isupov

Synopsis: The molecular-replacement method has been extended to locate macromolecular fragments in an electron-density map using a spherically averaged phased translation and a phased rotation function.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1457-1461  [ doi:10.1107/S0907444901010824 ]

Solution solution: using NMR models for molecular replacement

Y. W. Chen

Synopsis: An overview of the use of NMR models to solve crystal structures by molecular replacement is presented with particular emphasis on the preparation of search models. A recently developed protocol is tested and found to offer good results.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1462-1473  [ doi:10.1107/S0907444901008563 ]

Multidimensional molecular replacement

N. M. Glykos and M. Kokkinidis

Synopsis: A molecular-replacement method is described which simultaneously determines the rotational and translational parameters of all copies of a search model in the asymmetric unit of a target crystal structure.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1474-1479  [ doi:10.1107/S0907444901012458 ]

Molecular replacement by evolutionary search

C. R. Kissinger, D. K. Gehlhaar, B. A. Smith and D. Bouzida

Synopsis: Rapid six-dimensional molecular-replacement searches can be carried out using an evolutionary optimization algorithm. The performance of this algorithm and its dependence on search-model quality and target function are discussed.

Online 21 September 2001


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Acta Cryst. (2001). D57, 1480-1490  [ doi:10.1107/S0907444901013397 ]

Applications of anomalous scattering from S atoms for improved phasing of protein diffraction data collected at Cu K[alpha] wavelength

C. Yang and J. W. Pflugrath

Synopsis: The anomalous signal of S atoms can contribute to many aspects of solving protein structures and should be used routinely. For example, the anomalous scattering of sulfur was essential to solve the structure of trypsin which was initially phased from a single intrinsic Ca2+ ion in an SAS diffraction experiment.

Online 21 September 2001


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