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

Domain assignment for protein structures using a consensus approach: characterization and analysis

S Jones1, M Stewart, A Michie

  • 1Department of Biochemistry and Molecular Biology, University College, London, United Kingdom. sue@bsm.biochem.ucl.ac.uk

Protein Science : a Publication of the Protein Society
|April 1, 1998
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

Ross River virus transmission, infection, and disease: two and a half decades of research progress-an updated cross-disciplinary review.

Clinical microbiology reviews·2026
Same author

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.

Journal of cheminformatics·2024
Same author

Resolvin D2 promotes host defense in a 2 - hit model of sepsis with secondary lung infection.

Prostaglandins & other lipid mediators·2022
Same author

Lipoxin A4 promotes reduction and antibiotic efficacy against Pseudomonas aeruginosa biofilm.

Prostaglandins & other lipid mediators·2020
Same author

ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

F1000Research·2017
Same author

Clinical management of Brucella suis infection in dogs and implications for public health.

Australian veterinary journal·2017
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

A new consensus method improves protein domain assignment accuracy by combining algorithms. This approach achieves 100% accuracy when multiple methods agree, enhancing structural biology insights.

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Accurate assignment of structural domains in proteins is crucial for understanding protein function and evolution.
  • Existing automated methods for domain assignment vary in accuracy and coverage.

Purpose of the Study:

  • To develop and validate a consensus approach for protein domain assignment.
  • To improve the accuracy and reliability of automated protein domain identification.

Main Methods:

  • Combining multiple established domain assignment algorithms (PUU, DETECTIVE, DOMAK).
  • Evaluating the consensus approach on benchmark datasets with known assignments.
  • Applying the consensus method to a large dataset from the Protein Data Bank.

Related Experiment Videos

Main Results:

  • The consensus approach increased accuracy from 72% (individual algorithms) to 100% when all four tested methods agreed.
  • For a dataset of 787 protein chains, 55.7% of domain assignments were made automatically.
  • Of the automatically assigned domains, 13.5% represented multi-domain proteins.

Conclusions:

  • The consensus method significantly enhances the accuracy of protein domain assignment.
  • Even unassigned proteins by the consensus method often had correct domain boundaries identified by at least one algorithm.
  • Analysis of assigned domains revealed trends in size, secondary structure, and chain discontinuity.