Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Multi-resolution contour-based fitting of macromolecular structures.

Pablo Chacón1, Willy Wriggers

  • 1Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA. pchacon@scripps.edu

Journal of Molecular Biology
|April 2, 2002
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A Data Set of Paired Structural Segments Between Protein Data Bank and AlphaFold DB for Medium-Resolution Cryo-EM Density Maps: A Gap in Overall Structural Quality.

Bioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference)·2026
Same author

AlphaFold2 Model Refinement Using Structure Decoys.

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine·2026
Same author

Decoys Reveal Multiple Basins of Attraction for Cryo-Electron-Microscopy Flexible Fitting.

Computational structural bioinformatics : international workshop, CSBW 2024, Boston, MA, USA, November 16, 2024, proceeding. Computational Structural Bioinformatics Workshop (2024 : Boston, Mass.)·2025
Same author

Toward Modeling Protein Multimers by Combining AlphaFold 3 Predictions with Secondary Structures from Medium-Resolution Cryo-EM Maps.

Computational structural bioinformatics : international workshop, CSBW 2024, Boston, MA, USA, November 16, 2024, proceeding. Computational Structural Bioinformatics Workshop (2024 : Boston, Mass.)·2025
Same author

Tracing Randomly Oriented Filaments in a Simulated Actin Network Tomogram.

Proceedings. IEEE International Conference on Bioinformatics and Biomedicine·2025
Same author

Refinement of AlphaFold2 Models against Experimental Cryo-EM Density Maps at 4-6Å Resolution.

Proceedings. IEEE International Conference on Bioinformatics and Biomedicine·2025
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
Same journal

Structural basis for the pro-amyloidogenic action and ligand binding of a novel W72R variant of human apolipoprotein A-I.

Journal of molecular biology·2026
Same journal

Cryo-EM Structure of the C. elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.

Journal of molecular biology·2026
See all related articles

A new contour matching method improves molecular docking into low-resolution electron microscopy maps. This technique enhances precision for fitting components into large biomolecular assemblies, even at 30 Angstroms.

Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Accurate atomic model building into low-resolution cryo-electron microscopy (cryo-EM) maps remains a challenge.
  • Existing methods struggle with fitting smaller components into large macromolecular assemblies at resolutions below 15 Å.

Purpose of the Study:

  • To develop a novel contour-based matching criterion for quantitative docking of high-resolution structures into low-resolution cryo-EM maps.
  • To extend the resolution range of reliable component fitting into cryo-EM density maps.

Main Methods:

  • A Laplacian filter combined with a six-dimensional search using fast Fourier transforms (FFTs) was employed.
  • The algorithm rapidly scans rigid-body degrees of freedom for probe molecules against a target density map.

Related Experiment Videos

  • Docking performance was compared against the standard cross-correlation criterion.

    • Main Results:

    • The contour-based matching with the Laplacian filter extends correlation-based fitting to resolutions as low as 30 Å.
    • Significant gains in docking precision were observed at medium to low resolutions (15-30 Å).
    • A pseudo-atomic model of a microtubule was successfully constructed from a 20 Å resolution cryo-EM map.

    Conclusions:

    • The novel contour-based matching criterion significantly improves the accuracy of molecular docking into low-resolution cryo-EM maps.
    • This method enables reliable docking of smaller components into large biomolecular assemblies at resolutions previously inaccessible.
    • The approach facilitates the construction of accurate pseudo-atomic models from cryo-EM data, advancing structural biology.