Biomedical subjects

Laurent C Storoni

Publications and source records attributed to Laurent C Storoni.

4 recordsLinked to original sources

PubMed2005

Likelihood-enhanced fast translation functions.

This paper is a companion to a recent paper on fast rotation functions [Storoni et al. (2004), Acta Cryst. D60, 432-438], which showed how a Taylor-series expansion of the maximum-likelihood rotation function leads to improved likelihood-enhanced fast rotation functions. In a similar manner, it is shown here how linear and quadratic Taylor-series expansions and least-squares approximations of the maximum-likelihood translation function lead to likelihood-enhanced translation functions, which can be calculated by FFT and which are more sensitive to the correct translation than the traditional correlation-coefficient fast translation function. These likelihood-enhanced translation targets for molecular-replacement searches have been implemented in the program Phaser using the Computational Crystallography Toolbox (cctbx).

Bacterial Proteins↗

PubMed2004

Simple algorithm for a maximum-likelihood SAD function.

Recently, the multivariate complex normal distribution has been used to develop a maximum-likelihood probability function for single-wavelength anomalous diffraction phasing and refinement of heavy-atom parameters [Pannu & Read (2004), Acta Cryst. D60, 22-27]. The function accounts explicitly for the correlations between the observed and calculated Friedel mates and their errors. However, the method of derivation of the equation described by Pannu & Read (2004) leads to a complicated likelihood expression that suffers from a number of algorithmic limitations. Here, an alternative derivation of the P(SAD) function is described that leads to simplified algorithmic requirements and that allows an intuitive understanding of the expression.

Algorithms↗

PubMed2004

Likelihood-enhanced fast rotation functions.

Experiences with the molecular-replacement program Beast have shown that maximum-likelihood rotation targets are more sensitive to the correct orientation than traditional targets. However, this comes at a high computational cost: brute-force rotation searches can take hours or even days of computation time on current desktop computers. Series approximations to the full likelihood target have been developed that can be computed by fast Fourier transforms in minutes. These likelihood-enhanced targets are more sensitive to the correct orientation than the Crowther fast rotation function and they take advantage of information from partial solutions. The likelihood-enhanced rotation targets have been implemented in the program Phaser.

Algorithms↗

PubMed2003

Recent developments in the PHENIX software for automated crystallographic structure determination.

A new software system called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is being developed for the automation of crystallographic structure solution. This will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model, and facilitate structure solution for both the novice and expert crystallographer. Here, the features of PHENIXare reviewed and the recent advances in infrastructure and algorithms are briefly described.

Algorithms↗