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Related Experiment Video

Updated: Jun 3, 2026

The HoneyComb Paradigm for Research on Collective Human Behavior

The HoneyComb Paradigm for Research on Collective Human Behavior

Published on: January 19, 2019

Distributed structure determination at the JCSG.

Henry van den Bedem¹, Guenter Wolf, Qingping Xu

¹Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA. vdbedem@slac.stanford.edu

Acta Crystallographica. Section D, Biological Crystallography

|April 5, 2011

Summary

The automated Xsolve pipeline efficiently solved over 770 protein structures with 90% success, minimizing human intervention. Integrated tools like Consensus-Modeler and qFit further automated structure refinement for enhanced structural biology research.

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Last Updated: Jun 3, 2026

The HoneyComb Paradigm for Research on Collective Human Behavior

The HoneyComb Paradigm for Research on Collective Human Behavior

Published on: January 19, 2019

Area of Science:

Structural Biology
Computational Biology
Biochemistry

Background:

The Joint Center for Structural Genomics (JCSG) is a major center funded by the US Protein Structure Initiative (PSI).
Automated pipelines are crucial for high-throughput structure determination in structural biology.

Purpose of the Study:

To evaluate the performance and efficiency of the automated Xsolve pipeline for protein structure solution and refinement.
To demonstrate the effectiveness of integrated computational tools in minimizing human intervention during structure determination.

Main Methods:

Xsolve pipeline executed multiple crystallography software programs in parallel on a Linux cluster.
Consensus-Modeler was used to generate optimal models from multiple traces.
Xpleo and qFit were employed for automated fragment building and alternate conformation fitting.

Main Results:

Xsolve successfully solved, traced, and partially refined 90% of nearly 770 MAD/SAD structures at an average resolution of 2 Å.
The pipeline operated with minimal human intervention, showcasing high automation levels.
Integrated tools significantly reduced manual effort in structure refinement.

Conclusions:

The Xsolve pipeline is a highly effective and automated system for protein structure determination.
The integration of novel algorithms like Consensus-Modeler, Xpleo, and qFit enhances efficiency and accuracy in structural biology.
Automated pipelines are essential for advancing large-scale structural genomics efforts.