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

Flexible protein sequence patterns. A sensitive method to detect weak structural similarities.

G J Barton1, M J Sternberg

  • 1Biomedical Computing Unit, Imperial Cancer Research Fund Laboratories, Lincoln's Inn Fields, London, U.K.

Journal of Molecular Biology
|March 20, 1990
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

Identifying joint-specific gait mechanisms causing impaired gait in alkaptonuria patients.

Gait & posture·2021
Same author

Leaving hip rotation out of a conventional 3D gait model improves discrimination of pathological gait in cerebral palsy: A novel neural network analysis.

Gait & posture·2019
Same author

Data on items of AKUSSI in Alkaptonuria collected over three years from the United Kingdom National Alkaptonuria Centre and the impact of nitisinone.

Data in brief·2018
Same author

Nitisinone arrests ochronosis and decreases rate of progression of Alkaptonuria: Evaluation of the effect of nitisinone in the United Kingdom National Alkaptonuria Centre.

Molecular genetics and metabolism·2018
Same author

Substrate and flow characteristics associated with White Sturgeon recruitment in the Columbia River Basin.

Heliyon·2018
Same author

A marker based kinematic method of identifying initial contact during gait suitable for use in real-time visual feedback applications.

Gait & posture·2012
Same journal

Tesorai Search: cloud-based database search engine boosts identifications for mass spectrometry proteomics with a pretrained peptide-spectrum deep-learning model.

Journal of molecular biology·2026
Same journal

Characterization of diverse functions of NRF1 nuclear localization sequence.

Journal of molecular biology·2026
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
See all related articles

Flexible protein sequence patterns identify protein folds by defining residue positions and gaps. This method accurately distinguishes globin proteins, offering a powerful alternative to traditional sequence alignment techniques.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Conventional protein sequence analysis relies on rigid patterns or global/local alignments.
  • Identifying protein folds requires methods that account for evolutionary variations and structural constraints.

Purpose of the Study:

  • To introduce and evaluate a novel 'flexible protein sequence pattern' method for protein fold identification.
  • To compare the efficacy of flexible patterns against existing sequence alignment techniques.

Main Methods:

  • Development of a dynamic programming algorithm for flexible pattern matching.
  • Application of flexible patterns to the globin protein family, using structural alignment criteria.
  • Comparative analysis against single-sequence, multiple-sequence, and secondary structure-based alignment methods.

Related Experiment Videos

Main Results:

  • A flexible pattern from seven globins accurately identified all 345 globins in a database.
  • A pattern from human alpha-haemoglobin identified more globins than a standard global alignment method.
  • As few as 38 residue positions were sufficient to uniquely identify the globin fold.

Conclusions:

  • Flexible protein sequence patterns offer a powerful and efficient method for protein fold identification.
  • This approach effectively bridges the gap between simple pattern matching and complex sequence alignment algorithms.
  • The method's ability to define gaps and discard variable regions enhances its discriminatory power.