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

Prediction of operator-binding protein by discriminant analysis.

K Nakata1, J V Maizel

  • 1Laboratory of Mathematical Biology, National Cancer Institute, Frederick, Maryland.

Gene Analysis Techniques
|November 1, 1989
PubMed
Summary

This study introduces a novel method combining sequence analysis and protein properties to accurately identify DNA-binding regulatory proteins. The approach improves upon simple sequence patterns by integrating functional and structural data for better predictions.

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

Data mining of imperfect double-stranded RNA in 3' untranslated regions of eukaryotic mRNAs.

Biomolecular engineering·2007
Same author

Local thermodynamic stability scores are well represented by a non-central student's t distribution.

Journal of theoretical biology·2001
Same author

Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: a quantum chemical study.

Biophysical chemistry·2001
Same author

SDS polyacrylamide gel electrophoresis.

Trends in biochemical sciences·2000
Same author

Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape.

Proceedings of the National Academy of Sciences of the United States of America·2000
Same author

A gender-specific mRNA encoding a cytotoxic ribonuclease contains a 3' UTR of unusual length and structure.

Nucleic acids research·2000

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Protein Science

Background:

  • Operator-binding proteins share sequence similarities with known repressors (e.g., Cro, cI) and CAP protein.
  • These sequence patterns are not exclusive to DNA-binding proteins, leading to potential misidentification.
  • Accurate identification of DNA-binding regulatory proteins is crucial for understanding gene regulation.

Purpose of the Study:

  • To develop a more accurate method for identifying operator-binding proteins.
  • To differentiate true operator-binding proteins from those with similar but non-functional sequence patterns.
  • To enhance the prediction of DNA-binding regions in regulatory proteins.

Main Methods:

  • Utilized sequence analogy information combined with a pattern recognition algorithm.

Related Experiment Videos

  • Incorporated functional and structural protein properties: hydrophobicity, hydrophilicity, charged amino acids, electrostatic free energy, and helical structures.
  • Employed discriminant analysis to find optimal combinations of variables for prediction.

    • Main Results:

    • Identified a superior combination of sequence and structural variables for discriminating operator-binding proteins.
    • Successfully predicted DNA-binding regions in regulatory proteins not used in the initial training set, demonstrating predictive power.
    • The integrated approach showed improved accuracy over methods relying solely on sequence patterns.

    Conclusions:

    • A combined approach using sequence analogy, pattern recognition, and biophysical properties significantly enhances the identification of DNA-binding regulatory proteins.
    • This method offers a more robust tool for predicting protein function and DNA-binding capabilities.
    • The findings contribute to a better understanding of protein-DNA interactions and regulatory mechanisms.