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 Concept Videos

Molecular Models02:00

Molecular Models

44.1K
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.
44.1K
Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

3.0K
Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
3.0K

You might also read

Related Articles

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

Sort by
Same author

Lysozyme revisited: evaluating models of a reference protein in structural biology.

Current research in structural biology·2026
Same author

Mapping the Structure and Conformational Landscape of the 10-23 DNAzyme.

ACS chemical biology·2026
Same author

Crystallographic and EPR-based characterisation of Cu<sup>2+</sup>-binding to serum albumin: ATCUN coordination and additional sites.

Inorganic chemistry frontiers·2026
Same author

The incidence and outcomes of intraocular lens exchanges in patients dissatisfied with multifocal lenses: a 15-year retrospective dataset analysis.

Journal of cataract and refractive surgery·2026
Same author

Amplification-free one-pot RNA detection by pairing CRISPR-Cas13a with cascade amplification circuit-driven DNAzyme (RAPID).

Analytica chimica acta·2026
Same author

An atlas of plant viruses provides new insights into the diversity and evolution of the plant virome.

Plant disease·2026

Related Experiment Video

Updated: Feb 24, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

11.7K

Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and

Przemyslaw J Porebski1, Piotr Sroka1, Heping Zheng1

  • 1Department of Biological Physics & Molecular Physiology, University of Virginia, Charlottesville, Virginia.

Protein Science : a Publication of the Protein Society
|August 18, 2017
PubMed
Summary
This summary is machine-generated.

Molstack is a new platform for sharing biomolecular structures and their experimental evidence. It allows researchers to present, review, and publish structural data, improving reproducibility in science.

Keywords:
electron density interpretationmacromolecular crystallographyreproducibilitystructural biologyweb server

More Related Videos

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

12.3K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

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

Published on: July 19, 2024

2.2K

Related Experiment Videos

Last Updated: Feb 24, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

11.7K
Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

12.3K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

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

Published on: July 19, 2024

2.2K

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Macromolecular models, primarily derived from electron density maps, are foundational to understanding biomolecular structures.
  • The Protein Data Bank (PDB) disseminates these structures, but current quality metrics may not capture ambiguities in regions critical for function.
  • Suboptimal models can lead to inaccurate scientific conclusions, necessitating a closer examination of model-experimental agreement.

Purpose of the Study:

  • To introduce Molstack, a novel web-based platform for interactive publishing of structural data.
  • To facilitate the presentation and assessment of agreement between structural models and their corresponding experimental evidence (electron density maps).
  • To enhance reproducibility and collaboration in structural biology research.

Main Methods:

  • Development of Molstack, an interactive web platform for visualizing and sharing structural models and electron density maps.
  • Integration of features allowing users to present multiple interpretations, re-refinements, and corrections of structural data.
  • Design enabling researchers, reviewers, and readers to independently evaluate the experimental basis of structural conclusions.

Main Results:

  • Molstack provides a unified environment for presenting structural models alongside their raw experimental data (electron density maps).
  • The platform supports the display of diverse interpretations and refinements of structural data within a single interactive session.
  • It enables independent verification of structural models by enabling reviewers and readers to access and assess the underlying experimental evidence.

Conclusions:

  • Molstack addresses the critical need for transparently presenting the experimental evidence supporting macromolecular models.
  • The platform enhances scientific rigor by allowing independent assessment of model-data fit, thereby improving reproducibility.
  • Molstack fosters collaboration and hypothesis generation by providing a context for sharing and discussing structural interpretations and their evidential support.