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Updated: Dec 27, 2025

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

Published on: March 3, 2021

ALIXE: a phase-combination tool for fragment-based molecular replacement.

Claudia Millán¹, Elisabet Jiménez¹, Antonia Schuster²

¹Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain.

Acta Crystallographica. Section D, Structural Biology

|March 6, 2020

Summary

ALIXE enhances fragment-based molecular replacement by combining partial solutions for improved crystallographic model building. This optimized program efficiently groups consistent phases, aiding structure determination on standard hardware.

Keywords:

ALIXE ARCIMBOLDO combination fragment-based molecular replacement phasing

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Last Updated: Dec 27, 2025

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Area of Science:

Structural Biology
Crystallography
Computational Biology

Background:

Fragment-based molecular replacement (MBR) uses incomplete search models.
Accurate phase sets from fragment placement and refinement need combination for improved signal.

Purpose of the Study:

To describe the performance of the ALIXE program for combining partial MBR solutions.
To detail algorithm optimization for efficiency on modest hardware.

Main Methods:

ALIXE compares phase sets, evaluating mean phase differences to group consistent solutions.
Algorithm parallelization and redesign to handle typical solution landscapes.
Analysis of pairwise correlation between phase sets.

Main Results:

Optimized ALIXE algorithms improve performance for MBR.
Parallelization and redesign make ALIXE efficient on modest hardware.
ALIXE successfully analyzes, combines, and reduces redundant partial solutions.

Conclusions:

ALIXE is a valuable tool for enhancing MBR by effectively combining and refining partial solutions.
Optimized and parallelized ALIXE is efficient for crystallographic structure determination.
ALIXE is now integrated into ARCIMBOLDO programs, improving their functionality.