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

Assessing protein structures with a non-local atomic interaction energy

F Melo1, E Feytmans

  • 1Department of Biology, Laboratory of Structural Molecular Biology, Facultés Universitaires Notre-Dame de la Paix, Rue de Bruxelles 61, 5000 Namur, Belgium.

Journal of Molecular Biology
|May 22, 1998
PubMed
Summary

A new atomic mean force potential (AMFP) method accurately identifies errors in protein models and X-ray structures. This non-local energy profile (NL-profile) approach detects misalignments and stereochemical issues missed by other methods.

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

Influence of nanocellulose with different particle size on pasting and rheological properties of wheat starch.

International journal of biological macromolecules·2026
Same author

Predicting tearing paths in thin sheets.

Physical review. E·2019
Same author

Foam rheology at large deformation.

Physical review. E·2018
Same author

Effects of tetrahydrohyperforin in mouse hippocampal slices: neuroprotection, long-term potentiation and TRPC channels.

Current medicinal chemistry·2014
Same author

Elastic response and wrinkling onset of curved elastic membranes subjected to indentation test.

The European physical journal. E, Soft matter·2011
Same author

Novel α-ketoglutarate dioxygenase tfdA-related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides.

Environmental microbiology·2010

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Protein structure assessment is crucial for understanding biological function.
  • Existing methods often fail to detect subtle errors in protein models and experimental structures.
  • Accurate evaluation of protein structures is essential for drug discovery and molecular biology research.

Purpose of the Study:

  • To introduce a novel method for assessing protein structures based on non-local interaction energy.
  • To evaluate the sensitivity and accuracy of the atomic mean force potential (AMFP) in detecting errors.
  • To demonstrate the utility of the non-local energy profile (NL-profile) for both modeled and experimentally determined protein structures.

Main Methods:

  • Development and application of an atomic mean force potential (AMFP) to calculate non-local energy profiles (NL-profiles).

Related Experiment Videos

  • Evaluation of comparative protein models with known errors, including point errors and misalignments.
  • Assessment of a dataset of 143 X-ray solved protein structures, including those with unusual stereochemistry and refinement issues.

    • Main Results:

    • The AMFP-derived NL-profiles successfully identified point errors and misalignments in protein models that were missed by other methods.
    • A correlation was observed between decreasing resolution of X-ray structures and increasing average energy Z-scores.
    • The method accurately detected errors in structures refined in incorrect space groups and identified disordered residues.

    Conclusions:

    • The AMFP-based NL-profile method provides a sensitive and accurate approach for protein structure assessment.
    • This method is effective in identifying various types of errors in both computational models and experimental structures.
    • The ANOLEA program, implementing this method, is available online for broader scientific use.