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

Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Simon C Lovell1, Ian W Davis, W Bryan Arendall

  • 1Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

Proteins
|January 31, 2003
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

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

PLoS computational biology·2026
Same author

Domain-specific mechanisms of YAP1 variants in ocular coloboma revealed by in-vitro and organoid studies.

Biochimica et biophysica acta. Molecular basis of disease·2026
Same author

Structural Constraints Acting on the SARS-CoV-2 Spike Protein Reveal Limited Space for Viral Adaptation.

Genome biology and evolution·2026
Same author

From single-sequences to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2.

Nature communications·2026
Same author

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

Nucleic acids research·2026
Same author

Deciphering the Impact of Temperature on Pleiotropic Consequences of RNA Polymerase Mutations.

Molecular biology and evolution·2025
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

This study introduces a new C-beta deviation measure for protein structure validation, enhancing Ramachandran plots. It refines allowed and disallowed regions for amino acid conformations, improving accuracy for geometrical evaluations.

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biochemistry

Background:

  • Accurate geometrical validation is crucial for assessing protein structure quality.
  • Existing methods for analyzing protein conformations have limitations in sensitivity and accuracy.
  • Understanding allowed and disallowed regions in Ramachandran plots is key to interpreting protein structures.

Purpose of the Study:

  • To develop a new C-beta deviation measure for enhanced geometrical validation of protein structures.
  • To create updated, high-resolution Ramachandran plots with improved delineation of allowed and disfavored regions.
  • To investigate discrepancies between theoretical predictions and empirical data for amino acid conformations.

Main Methods:

  • Developed a novel C-beta deviation measure based on the deviation of the C-beta atom from its ideal position.

Related Experiment Videos

  • Generated density-dependent smoothed phi,psi plots using a large dataset of high-resolution protein structures (81,234 residues).
  • Analyzed specific conformations, such as gamma-turns, and compared empirical data with theoretical calculations.

    • Main Results:

    • The C-beta deviation measure effectively encapsulates major structure validation information from bond angle distortions.
    • Updated Ramachandran plots show sharp boundaries and clear distinctions between allowed, disfavored, and forbidden regions for various amino acid types.
    • Identified the gamma-turn conformation as occurring in well-ordered regions and near functional sites, contrary to some validation programs.
    • Empirical distributions for Glycine, Proline, and pre-Proline residues were defined, and discrepancies with theoretical predictions were highlighted.

    Conclusions:

    • The new C-beta deviation measure and updated Ramachandran plots provide more accurate tools for protein structure validation.
    • The findings challenge existing assumptions about certain conformations and highlight the need for refined theoretical models.
    • Tools like MOLPROBITY and RAMPAGE are available for users to perform these geometrical evaluations.