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Updated: Mar 14, 2026

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

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Published on: July 19, 2024

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density

Guray Kuzu¹, Ozlem Keskin¹, Ruth Nussinov²

¹Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey.

Acta Crystallographica. Section D, Structural Biology

|October 7, 2016

Summary

PRISM-EM computationally generates protein assembly models by combining crystallography and 3D electron microscopy (3DEM) data. This new method accurately predicts complex structures, aiding molecular biology research.

Keywords:

PRISM-EM modelling protein assemblies multimolecular protein complexes protein structure prediction three-dimensional electron microscopy

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Area of Science:

Structural biology
Molecular and cellular biology

Background:

Protein assemblies are crucial for cellular processes.
Three-dimensional electron microscopy (3DEM) is vital for determining structures, especially for those difficult to crystallize.

Purpose of the Study:

To introduce PRISM-EM, a novel computational method for generating protein assembly models.
To validate the accuracy and compare PRISM-EM with existing methods.

Main Methods:

PRISM-EM combines crystallographic data with 3DEM density maps.
Model accuracy was assessed using backbone deviations (<5 Å) and benchmark datasets.
Performance was compared against other computational methods.

Main Results:

PRISM-EM successfully generated plausible structural models.
Validated predictions showed high accuracy against known crystallographic complexes.
The method demonstrated strong correlation with EM density maps and interface predictions.

Conclusions:

PRISM-EM offers a robust approach for modeling protein assemblies.
The method enhances the utility of 3DEM data for structural determination.
PRISM-EM was applied to predict the structure of the HIV-1 envelope glycoprotein complex.