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

MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.

Ian W Davis1, Laura Weston Murray, Jane S Richardson

  • 1Department of Biochemistry, Duke University, Durham, NC 27710-3711, USA.

Nucleic Acids Research
|June 25, 2004
PubMed
Summary

MolProbity provides comprehensive quality validation for 3D molecular structures, including proteins and nucleic acids. It identifies steric issues and analyzes atomic contacts, offering detailed H-bond and van der Waals interactions for enhanced structural analysis.

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

RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.

PLoS computational biology·2026
Same author

New targets and procedures for validating the valence geometry of nucleic acid structures.

Nucleic acids research·2026
Same author

Categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures: near-predictive, pseudostructure and barbed wire.

Acta crystallographica. Section D, Structural biology·2025
Same author

Categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures.

bioRxiv : the preprint server for biology·2025
Same author

Cis-nonProline peptides: Genuine occurrences and their functional roles.

Protein science : a publication of the Protein Society·2025
Same author

Computationally derived RNA polymerase III promoters enable maize genome editing.

Frontiers in plant science·2025

Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Bioinformatics

Background:

  • Accurate three-dimensional (3D) structures are crucial for understanding molecular function.
  • Quality validation of these structures is essential to ensure reliability in research.
  • Existing methods may not offer comprehensive analysis of atomic interactions and steric clashes.

Purpose of the Study:

  • To introduce MolProbity, a versatile web service for the quality assessment of macromolecular structures.
  • To provide detailed analysis of steric problems and atomic contacts within protein, nucleic acid, and complex structures.
  • To offer advanced visualization tools for exploring molecular interfaces and hydrogen bonding networks.

Main Methods:

  • Utilizes all-atom contact analysis to detect steric hindrances.

Related Experiment Videos

  • Calculates and visualizes hydrogen bonds and van der Waals contacts at component interfaces.
  • Performs addition and optimization of all hydrogen atoms (polar and nonpolar).
  • Integrates the KiNG viewer for interactive 3D kinemage visualizations.

    • Main Results:

    • MolProbity provides overall numeric scores for structure quality.
    • Detailed lists of steric problems and contact analyses are generated.
    • Downloadable PDB and graphics files are available.
    • Informative, manipulable 3D kinemage graphics offer on-line visualization.

    Conclusions:

    • MolProbity serves as a valuable, free resource for researchers needing to validate and analyze macromolecular structures.
    • The service enhances the reliability of structural data through rigorous quality checks.
    • Interactive 3D visualizations facilitate a deeper understanding of molecular interactions and structural integrity.