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

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining.

Taner Z Sen1, Haitao Cheng, Andrzej Kloczkowski

  • 1Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011-3020, USA. taner@iastate.edu

Protein Science : a Publication of the Protein Society
|September 27, 2006
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

Proteome-wide analysis of protein stability in Escherichia coli under acid stress.

Journal of industrial microbiology & biotechnology·2026
Same author

Chiral π-conjugated polymer films <i>via</i> kinetically controlled dip-coating for circularly polarized light information encoding.

Nanoscale·2026
Same author

Protein language models accurately predict polymorphic peptide-modulated NK cell receptor-HLA class I interaction strengths.

Science advances·2026
Same author

Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse.

Scientific data·2026
Same author

Assessment of miRNAs as transcriptional regulators in respiratory syncytial virus infection through computational analysis and molecular docking studies.

PloS one·2026
Same author

A Comparative Study on the Identification of Xanthium sibiricum Patrin ex Widder and Xanthium italicum Moretti Based on Three Microscopy Technology.

Microscopy research and technique·2026
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 hybrid algorithm, Consensus Data Mining (CDM), improves protein secondary structure prediction accuracy. By combining Fragment Database Mining (FDM) and GOR V, CDM achieves up to 93.2% accuracy, surpassing existing methods.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Protein tertiary structure prediction accuracy is crucial for biological research.
  • Current secondary structure prediction methods often yield accuracy below 80%.
  • Improved secondary structure prediction can significantly benefit various protein modeling techniques.

Purpose of the Study:

  • To develop a novel hybrid algorithm for enhanced protein secondary structure prediction.
  • To improve upon existing secondary structure prediction accuracies.
  • To integrate Fragment Database Mining (FDM) and GOR V methods into a consensus approach.

Main Methods:

  • Developed a hybrid algorithm, Consensus Data Mining (CDM).
  • CDM combines Fragment Database Mining (FDM) and GOR V (information theory, Bayesian statistics, MSA).

Related Experiment Videos

  • The algorithm dissects sequences into fragments, comparing them to Protein Data Bank (PDB) structures and using GOR V for remaining fragments.

    • Main Results:

    • CDM accuracy, measured by Q(3), ranges from 67.5% to 93.2%.
    • Optimal performance is achieved with a 50% sequence identity threshold.
    • Accuracy is dependent on the availability of high-sequence-identity structural fragments in the PDB.

    Conclusions:

    • The Consensus Data Mining (CDM) algorithm offers a significant improvement in protein secondary structure prediction.
    • The method's accuracy is expected to increase as the Protein Data Bank expands.
    • CDM provides a robust approach by leveraging both database mining and information theory.