Rotations and rotation matrices

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

Molecular replacement – historical background

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

Implementation of molecular replacement in AMoRe

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

Pushing the boundaries of molecular replacement with maximum likelihood

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

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

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.

Patterson correlation methods: a review of molecular replacement with CNS

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

NMR trial models: experiences with the colicin immunity protein Im7 and the p85α C-terminal SH2–peptide complex

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 p85α subunit of human phosphatidylinositol 3-OH kinase complexed to a PDGF receptor-derived specificity peptide.

Using electron-microscopy images as a model for molecular replacement

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

Phasing from an envelope

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

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

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

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

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

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

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.

Fast Fourier feature recognition

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.

ARP/wARP and molecular replacement

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.

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

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.

Solution solution: using NMR models for molecular replacement

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.

Multidimensional molecular replacement

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.

Molecular replacement by evolutionary search

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.

Applications of anomalous scattering from S atoms for improved phasing of protein diffraction data collected at Cu Kα wavelength

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.