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Updated: May 17, 2026

Application of Monolayer Graphene to Cryo-Electron Microscopy Grids for High-resolution Structure Determination

Application of Monolayer Graphene to Cryo-Electron Microscopy Grids for High-resolution Structure Determination

Published on: November 10, 2023

GRID: a high-resolution protein structure refinement algorithm.

Mohsen Chitsaz¹, Stephen L Mayo

¹Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, California 91125, USA.

Journal of Computational Chemistry

|October 16, 2012

Summary

This summary is machine-generated.

We developed GRID, a new algorithm for refining protein structures. GRID significantly improves protein structure energy more effectively than the Backrub algorithm using similar computational resources.

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Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Energy-based refinement of protein structures is crucial for atomic-level accuracy.
Accurate refinement depends on reliable force fields and efficient conformational search algorithms.

Purpose of the Study:

To develop and evaluate a high-resolution protein structure refinement algorithm named GRID.
To compare the performance of GRID against the Backrub algorithm in terms of energy improvement and computational efficiency.

Main Methods:

Developed the GRID algorithm for high-resolution protein structure refinement.
Systematically perturbed backbone dihedrals and side-chain rotamer conformations using an all-atom force field.
Compared GRID with the Backrub algorithm on 10 high-resolution crystal structures from the Protein Data Bank.

Main Results:

GRID achieved significantly better energy improvements compared to Backrub.
Both GRID and Backrub required similar computational resources.
GRID-refined structures showed slightly higher backbone RMSD (0.25 ± 0.02 Å) than Backrub (0.14 ± 0.04 Å), indicating preserved topology.

Conclusions:

GRID is an effective high-resolution refinement algorithm for protein structures.
GRID offers superior energy optimization compared to Backrub while maintaining comparable computational costs.
Both algorithms successfully preserve the overall topology of the refined protein structures.