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

Folding pattern recognition in proteins using spectral analysis methods.

Carlos A Del Carpio-Munoz1, Julio Cesar Carbajal

  • 1Laboratory for Bioinformatics Department of Ecological Engineering, Toyohashi University of Technology, Tempaku, Toyohashi 441-8580, Japan. carlos@translell.eco.tut.ac.jp

Genome Informatics. International Conference on Genome Informatics
|October 23, 2003
PubMed
Summary

This study introduces a novel sequence homology method for protein folding prediction. It effectively identifies structural similarities in proteins with low sequence homology, outperforming traditional methods in the "twilight zone".

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same journal

Linear regression models predicting strength of transcriptional activity of promoters.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

Sign: large-scale gene network estimation environment for high performance computing.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

Docking-calculation-based method for predicting protein-RNA interactions.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

Mechanism of cell cycle disruption by multiple p53 pulses.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

Database for crude drugs and Kampo medicine.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

A dynamic programming algorithm to predict synthesis processes of tree-structured compounds with graph grammar.

Genome informatics. International Conference on Genome Informatics·2011

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Traditional protein folding prediction relies on sequence alignment, which struggles with distantly related proteins due to evolutionary sequence divergence.
  • The 'twilight zone' of sequence homology (20-30% similarity) presents a challenge, where proteins share structure and function but have low sequence homology.
  • Existing methods face limitations in homolog coverage, impacting their performance in detecting subtle similarities.

Purpose of the Study:

  • To propose a novel strategy for detecting protein structural and folding similarities.
  • To overcome the limitations of sequence alignment-based homology methodologies.
  • To improve protein folding prediction, particularly for proteins in the twilight zone of homology.

Main Methods:

Related Experiment Videos

  • A new concept of sequence homology based on periodicity analysis of residue physicochemical properties.
  • Utilizing a front-end processing technique from automatic speech recognition to compute the cepstrum.
  • Deriving sequence homology through the alignment of spectral envelopes derived from cepstral analysis.

Main Results:

  • The proposed method successfully detects homology by aligning spectral envelopes, revealing similarities in proteins with low sequence homology.
  • This approach effectively identifies proteins with common folding patterns and biological functions despite limited sequence similarity.
  • The methodology demonstrates superior performance compared to existing methods in the challenging twilight zone of sequence homology.

Conclusions:

  • The novel sequence homology strategy based on physicochemical property periodicity offers a powerful alternative for protein folding prediction.
  • This method enhances the ability to identify structurally and functionally related proteins with low sequence homology.
  • The approach shows significant promise for advancing protein structure prediction and bioinformatics research, especially in the twilight zone.