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Related Concept Videos

Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

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Related Experiment Video

Updated: May 21, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps.

Matthew L Baker1, Mariah R Baker, Corey F Hryc

  • 1Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA. mbaker@bcm.edu

Biopolymers
|June 15, 2012
PubMed
Summary
This summary is machine-generated.

New computational tools, Pathwalking and Gorgon, enable accurate modeling of protein structures from subnanometer resolution cryo-electron microscopy (cryo-EM) density maps, aiding cellular function research.

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Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
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Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Macromolecular complexes are vital for cellular functions.
  • X-ray crystallography and cryo-electron microscopy (cryo-EM) image these complexes, but often at limited resolutions.
  • Few tools exist for modeling structures at 3-10 Å resolution.

Purpose of the Study:

  • To develop novel computational utilities for modeling and annotating macromolecular structures at subnanometer resolution.
  • To address the limitations of existing tools for analyzing low-resolution cryo-EM data.

Main Methods:

  • Development of de novo modeling tools: Pathwalking and Gorgon.
  • Implementation of secondary structure identification tool (SSEHunter).
  • Integration of rigid-body/flexible fitting within Gorgon.

Main Results:

  • Demonstrated Pathwalking, Gorgon, and SSEHunter in the 2010 Cryo-EM Modeling Challenge.
  • Submitted 30 structural models from ten subnanometer resolution datasets.
  • Achieved accurate structural models and annotations across diverse density maps.

Conclusions:

  • The developed utilities provide a robust toolkit for analyzing protein structures in macromolecular assemblies at non-atomic resolutions.
  • These tools enhance the interpretation of subnanometer resolution cryo-EM data.
  • Facilitates a deeper understanding of cellular mechanisms through structural modeling.