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

Issues in high-throughput comparative modelling: a case study using the ubiquitin E2 conjugating enzymes.

P J Winn1, J N D Battey, K Schleinkofer

  • 1European Molecular Biology Laboratory, Heidelberg, Germany. winn@embl-heidelberg.de <winn@embl-heidelberg.de>

Proteins
|November 24, 2004
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

First crystallographic signature of amyloid-like fibril forming beta-sheet assemblage from a tripeptide with non-coded amino acids.

Chemical communications (Cambridge, England)·2002
Same author

Audit of stapedectomy results in a district general hospital.

Clinical otolaryngology and allied sciences·2002
Same author

Coronary artery disease and its problems in management.

Journal of the Indian Medical Association·2002
Same author

Leucopenia in adult polycystic kidney disease patients on haemodialysis.

Nephron·2002
Same author

Traditional healers and their practices in Malawi.

Tropical doctor·2002
Same author

Enhanced frequency of micronuclei in individuals exposed to arsenic through drinking water in West Bengal, India.

Mutation research·2002

High-throughput protein structure modeling for ubiquitin-conjugating enzyme (UBC or E2) families was improved by using single, high-identity templates and rigorous quality checking. This approach enhances the accuracy of comparative modeling for structural and electrostatic potential analysis.

Area of Science:

  • Structural biology
  • Computational biology
  • Biochemistry

Background:

  • Comparative modeling is crucial for predicting protein structures.
  • High-throughput methods face challenges in accuracy and consistency.
  • Ubiquitin-conjugating enzymes (UBC or E2) are vital in cellular processes.

Purpose of the Study:

  • To investigate and resolve issues in high-throughput comparative protein structure modeling.
  • To develop a robust method for modeling the ubiquitin-conjugating enzyme (UBC or E2) family.
  • To enable accurate structural and electrostatic potential comparisons.

Main Methods:

  • A semi-automatic modeling method was developed, emphasizing structural comparison quality.
  • Structural and sequence features of the E2 family were utilized to refine sequence alignment and template selection.

Related Experiment Videos

  • Rigorous quality checking was implemented to identify and reject anomalous models.

    • Main Results:

    • Using a single template with the highest sequence identity yielded models comparable to those from multiple templates.
    • Quality checking successfully identified and removed models with structural anomalies.
    • The refined modeling approach allowed for effective comparison of UBC structural features and electrostatic potentials.

    Conclusions:

    • Optimized comparative modeling using single, high-identity templates and quality control is effective for the UBC family.
    • A fully automated pipeline was developed for high-throughput identification, modeling, and analysis of E2 sequences.
    • This work provides a reliable method for structural and functional insights into protein families.