Jove
Visualize
Contact Us

Related Experiment Videos

Dead-end based modeling tools to explore the sequence space that is compatible with a given scaffold

I Lasters1, J Desmet, M De Maeyer

  • 1Center for Transgene Technology and Gene Therapy, Fianders Interuniversity Institute for Biotechnology, K.U. Leuven, Belgium.

Journal of Protein Chemistry
|July 1, 1997
PubMed
Summary

The dead-end elimination algorithm efficiently finds protein structures. This study enhances the algorithm for better sequence compatibility and packing predictions in protein cores.

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

Endoscopic diagnosis of a colonic localisation of a mantle cell lymphoma.

Acta gastro-enterologica Belgica·2022
Same author

Ten-year outcomes after primary vertical sleeve gastrectomy for morbid obesity: a monocentric cohort study.

Surgical endoscopy·2020
Same author

Olmesartan-induced enteropathy treated with budesonide.

Acta gastro-enterologica Belgica·2019
Same author

Caramel colour and process by-products in foods and beverages: Part I - Development of a UPLC-MS/MS isotope dilution method for determination of 2-acetyl-4-(1,2,3,4-tetrahydroxybutyl)imidazole (THI), 4-methylimidazole (4-MEI) and 2-methylimidazol (2-MEI).

Food chemistry·2018
Same author

Caramel colour and process contaminants in foods and beverages: Part II - Occurrence data and exposure assessment of 2-acetyl-4-(1,2,3,4-tetrahydroxybutyl)imidazole (THI) and 4-methylimidazole (4-MEI) in Belgium.

Food chemistry·2018
Same author

Assessment of predictive factors for recurrence in laparoscopic ventral hernia repair using a bridging technique.

Surgical endoscopy·2017
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

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • The dead-end elimination (DEE) algorithm is crucial for determining the global minimum-energy conformation (GMEC) of protein side chains with fixed backbones.
  • Efficiently calculating GMEC is vital for protein homology modeling and understanding protein structure-function relationships.

Purpose of the Study:

  • To enhance the efficacy of the DEE algorithm using logical arguments.
  • To explore DEE's application in identifying sequences compatible with specific protein scaffolds.
  • To investigate properties of GMEC structures for predicting protein core packing.

Main Methods:

  • The study refines the DEE algorithm with advanced logical arguments.
  • Theoretical considerations are applied to assess sequence-scaffold compatibility using DEE.

Related Experiment Videos

  • Analysis of GMEC structures involves evaluating nonbonded energy, accessible surface area, and conformational deviations.

    • Main Results:

    • The enhanced DEE algorithm shows increased efficiency in conformational searches.
    • New theoretical insights are provided for predicting sequence compatibility with protein scaffolds.
    • Properties derived from GMEC structures demonstrate potential for predicting core packing success.

    Conclusions:

    • The dead-end elimination algorithm is a powerful tool for protein structure prediction and analysis.
    • The study advances DEE's utility in sequence compatibility and protein core packing predictions.
    • Investigating GMEC properties offers a novel approach to understanding protein sequence-structure relationships.