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Updated: Jun 23, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Automated multiconformer model building for X-ray crystallography and cryo-EM.

Stephanie A Wankowicz¹, Ashraya Ravikumar¹, Shivani Sharma^2,3

¹Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.

|June 21, 2024

Summary

qFit software now models protein conformational heterogeneity in structural biology. This automated strategy improves biomolecular models, reflecting experimental data more accurately and advancing studies on dynamics and function.

Keywords:

X-ray crystallography conformational heterogeneity cryo-EM molecular biophysics none protein dynamics structural biology

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Area of Science:

Structural biology
Computational biology
Biophysics

Background:

Biomolecules exist in multiple functional conformational states.
Traditional methods like X-ray crystallography and cryo-EM yield ensemble-averaged data.
Current models often represent only a single conformation, missing structural complexity.

Purpose of the Study:

To address the need for modeling structural ensembles that accurately reflect experimental data.
To introduce enhanced qFit software for automated modeling of protein conformational heterogeneity.
To improve the representation of biomolecular structural diversity.

Main Methods:

Enhancements to the qFit automated computational strategy.
Incorporating protein conformational heterogeneity into models built into density maps.
Utilizing superior Rfree and geometry metrics for validation.

Main Results:

qFit produces multiconformer models that capture conformational heterogeneity.
Algorithmic improvements lead to superior Rfree and geometry metrics.
Models are compatible with standard model building and refinement software.

Conclusions:

qFit reduces the difficulty of creating multiconformer models.
This facilitates the development of new hypotheses on macromolecular dynamics and function.
Enables more accurate representation of biomolecular structural diversity.