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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

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Published on: October 19, 2021

MrBUMP: an automated pipeline for molecular replacement.

Ronan M Keegan¹, Martyn D Winn

¹Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, England.

Acta Crystallographica. Section D, Biological Crystallography

|December 21, 2007

Summary

A new automated pipeline simplifies macromolecular structure determination using molecular replacement. It efficiently finds and prepares search models, aiding both routine and challenging crystallography cases.

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Area of Science:

Structural Biology
Computational Biology
Crystallography

Background:

Macromolecular structure solution is crucial for understanding biological processes.
Molecular replacement is a key technique for determining protein structures.
Automating complex computational pipelines can accelerate structure determination.

Purpose of the Study:

To describe a novel automated pipeline for macromolecular structure solution.
To emphasize the discovery and preparation of diverse search models for molecular replacement.
To enhance the efficiency and success rate of molecular replacement, particularly for difficult cases.

Main Methods:

Development of an automation pipeline for molecular replacement.
Systematic generation and selection of numerous search models.
Integration of pipeline with core molecular replacement programs.
Highlighting recent functional additions to the MrBUMP software.

Main Results:

The pipeline automates routine crystallographic tasks, offering convenience.
For challenging structures, the pipeline identifies optimal template structures and model edits.
The system can discover effective search model combinations that might be overlooked manually.
MrBUMP's enhanced functionality is demonstrated.

Conclusions:

The described pipeline streamlines macromolecular structure solution via molecular replacement.
Automated search model generation improves efficiency and success rates in crystallography.
The tool is valuable for both standard and complex structure determination challenges.