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

Secondary structure prediction using segment similarity

L Rychlewski1, A Godzik

  • 1The Scripps Research Institute, Department of Molecular Biology, La Jolla, CA 92037, USA.

Protein Engineering
|March 6, 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

Expanding the set of rhodococcal Baeyer-Villiger monooxygenases by high-throughput cloning, expression and substrate screening.

Applied microbiology and biotechnology·2012
Same author

Computational protein function prediction: are we making progress?

Cellular and molecular life sciences : CMLS·2007
Same author

The status of structural genomics defined through the analysis of current targets and structures.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2004
Same author

The apoptosis database.

Cell death and differentiation·2003
Same author

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Nature·2002
Same author

CAFASP2: the second critical assessment of fully automated structure prediction methods.

Proteins·2002
Same journal

Structure of a human Rhinovirus complexed with its receptor molecule.

Protein engineering·2024
Same journal

pH-responsive polymer-assisted refolding of urea- and organic solvent-denatured alpha-chymotrypsin.

Protein engineering·2004
Same journal

Evaluation of different linker regions for multimerization and coupling chemistry for immobilization of a proteinaceous affinity ligand.

Protein engineering·2004
Same journal

Recombinant porcine intestinal carboxylesterase: cloning from the pig liver esterase gene by site-directed mutagenesis, functional expression and characterization.

Protein engineering·2004
Same journal

Periplasmic expression of human growth hormone via plasmid vectors containing the lambdaPL promoter: use of HPLC for product quantification.

Protein engineering·2004
Same journal

Shift of fibril-forming ability of the designed alpha-helical coiled-coil peptides into the physiological pH region.

Protein engineering·2004
See all related articles

This study introduces a novel protein secondary structure prediction method. It achieves 72.4% accuracy by comparing sequence segments against a database of known protein structures.

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate prediction of protein secondary structure is crucial for understanding protein function and design.
  • Existing methods often face challenges with accuracy and generalization across diverse protein families.

Purpose of the Study:

  • To develop and validate a novel, accurate, and extensible method for predicting protein secondary structure.
  • To leverage sequence and structural information from known proteins to predict the secondary structure of novel sequences.

Main Methods:

  • A secondary structure prediction method was developed using sequence segment similarity.
  • A genetic algorithm optimized a similarity matrix (21x40) comparing target sequences with database entries based on sequence and burial status.

Related Experiment Videos

  • The method was evaluated on non-homologous Protein Data Bank (PDB) datasets, CASP2 targets, and new PDB structures.

    • Main Results:

    • The prediction method achieved 72.4% accuracy on a non-homologous dataset (max sequence identity <25%).
    • The accuracy was consistently reproduced on independent test sets, including CASP2 targets and recent PDB structures.
    • The method demonstrated robustness, with minimal accuracy decrease even when excluding related protein folds from the database.

    Conclusions:

    • The developed method provides a reliable approach for protein secondary structure prediction.
    • Its open architecture facilitates extensions for other prediction types and structural analysis.
    • The findings highlight the effectiveness of segment similarity and optimized comparison metrics in secondary structure prediction.