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

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.

R Landgraf1, I Xenarios, D Eisenberg

  • 1UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, 405 Hilgard Avenue, Los Angeles, CA, 90095-1570, USA.

Journal of Molecular Biology
|April 9, 2001
PubMed
Summary

Three-dimensional cluster analysis predicts functional residue clusters in proteins by analyzing evolutionary variation and structural environments. This method accurately identifies important protein interfaces, especially transient ones.

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

An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Database : the journal of biological databases and curation·2019
Same author

Paternal Age and Transgenerational Telomere Length Maintenance: A Simulation Model.

Scientific reports·2019
Same author

Clinical Evaluation of the Cepheid Xpert TV Assay for Detection of Trichomonas vaginalis with Prospectively Collected Specimens from Men and Women.

Journal of clinical microbiology·2017
Same author

A Health Services Research Agenda for Bariatric Surgery Within the Veterans Health Administration.

Journal of general internal medicine·2017
Same author

Increased Accuracy of Distribution Based Missing Value Imputation: An Alternative to Mean Inputation in Real World Environment Survey Research.

Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research·2016
Same author

Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps.

Molecular ecology·2014

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein science

Background:

  • Predicting functional residue clusters is crucial for understanding protein mechanisms.
  • Existing methods often lack the integration of 3D structural information with evolutionary data.

Purpose of the Study:

  • To introduce and evaluate a novel three-dimensional (3D) cluster analysis method for predicting functional residue clusters in proteins.
  • To assess the efficacy of the regional conservation score (C(R)(x)) in identifying functionally relevant residue clusters, including poorly conserved interfaces.

Main Methods:

  • Input data includes a representative protein structure and a multiple sequence alignment.
  • Residues are represented by regional alignments capturing structural and evolutionary context.

Related Experiment Videos

  • Calculation of global and regional similarity matrices to derive regional conservation (C(R)(x)) and similarity deviation (S(x)) scores for each residue.

    • Main Results:

    • The regional conservation score (C(R)(x)) outperforms methods lacking 3D information for identifying functional residue clusters.
    • C(R)(x) is particularly effective for predicting poorly conserved, transient protein-protein interfaces.
    • Similarity deviation scores correlate with specificity-conferring regions, highlighting functionally relevant spatial clusters.

    Conclusions:

    • 3D cluster analysis provides an effective and easily applicable method for predicting functionally relevant spatial residue clusters.
    • The regional conservation score (C(R)(x)) is a valuable metric for identifying critical residues and interfaces in proteins.
    • The method aids in understanding protein function and specificity through evolutionary and structural insights.