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Related Experiment Video

Updated: Jun 10, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.

Suparno Nandi1, Graeme L Conn1

  • 1Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States.

Journal of Chemical Information and Modeling
|June 9, 2026
PubMed
Summary
This summary is machine-generated.

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Cryo-electron Microscopy01:28

Cryo-electron Microscopy

Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...

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KNexPHENIX refines macromolecular structures using a novel workflow, improving model quality for cryo-electron microscopy and X-ray crystallography. This method enhances stereochemistry without compromising accuracy or causing overfitting.

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Accurate atomic models of macromolecules are crucial for understanding biological function.
  • Current refinement methods face efficiency limitations, hindering the generation of high-quality structural data.
  • The Protein Data Bank requires improved models for deposited structures.

Purpose of the Study:

  • To develop an efficient and accessible workflow for refining macromolecular structures.
  • To improve the stereochemical quality of atomic models derived from experimental data.
  • To provide a practical tool for both cryo-electron microscopy (cryo-EM) and X-ray crystallography.

Main Methods:

  • Development of KNexPHENIX, a PHENIX-based workflow.
  • Integration of staged refinement, geometry minimization, and customized parameters.

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Related Experiment Videos

Last Updated: Jun 10, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Cryo-EM and Single-Particle Analysis with Scipion
09:06

Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

  • Evaluation on deposited and de novo models from various sources.

    • Main Results:

    • KNexPHENIX consistently produced models with lower MolProbity scores, indicating improved stereochemistry.
    • The workflow maintained model-to-map correlation for cryo-EM data.
    • For X-ray crystallography, Rfree-Rwork difference was maintained or reduced, limiting overfitting.

    Conclusions:

    • KNexPHENIX offers a practical and accessible approach for refining macromolecular structures.
    • The workflow enhances model quality for both cryo-EM and X-ray crystallography.
    • Improved models generated by KNexPHENIX facilitate better structural information deposition.