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

Grammatical representations of macromolecular structure.

David Chiang1, Aravind K Joshi, David B Searls

  • 1Information Sciences Institute, University of Southern California, Marina del Rey, California 90292, USA. chiang@isi.edu

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|June 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

Intestinal Stem Cells From Patients With Inflammatory Bowel Disease Retain an Epigenetic Memory of Inflammation.

Cellular and molecular gastroenterology and hepatology·2026
Same author

Treg-specific IL-6R signaling: a novel role in the regulation of the intestinal epithelium.

American journal of physiology. Gastrointestinal and liver physiology·2025
Same author

Intestinal Stem Cells from Patients with Inflammatory Bowel Disease Retain an Epigenetic Memory of Inflammation.

bioRxiv : the preprint server for biology·2025
Same author

19-Year-Old Man With Abdominal Pain, Vomiting, Bloody Diarrhea, and Rash.

Mayo Clinic proceedings·2024
Same author

Unraveling function and diversity of bacterial lectins in the human microbiome.

Nature communications·2022
Same author

Dietary manipulation of the gut microbiome in inflammatory bowel disease patients: Pilot study.

Gut microbes·2022
Same journal

Mosquito Species and Gender Identification System Based on Artificial Intelligence and Image Processing Methods.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

GMSA: A Graph Matching and Point Cloud Registration-Based Method for Spatial Transcriptomics Data Alignment.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Investigations on Multiple Protein Scaffold Filling.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Cell Type Prediction for Single-Cell RNA Sequencing Utilizing Unsupervised Domain Adaptation and Semi-Supervised Learning.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

PPIGAN: Prediction of Protein-Protein Interactions Using Generative Adversarial Networks.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Deep Structure-Enhanced Cell Clustering Model for Single-Cell RNA Sequencing Data.

Journal of computational biology : a journal of computational molecular cell biology·2026
See all related articles

Computational linguistics methods for RNA and protein structure modeling share core principles. These can be unified within tree-adjoining grammars, enabling novel extensions for structure analysis.

Area of Science:

  • Computational biology
  • Bioinformatics
  • Computational linguistics

Background:

  • Context-free grammars were first applied to RNA secondary structures in 1988.
  • Numerous ad hoc and formal methods from computational linguistics have since been used to model RNA and protein structure.

Purpose of the Study:

  • To demonstrate that most existing methods for modeling RNA and protein structure share common underlying principles.
  • To show these methods can be unified within the framework of tree-adjoining grammars.
  • To propose novel extensions to these core principles.

Main Methods:

  • Analysis of existing computational linguistics methods applied to biological structures.
  • Formalization of these methods within the framework of tree-adjoining grammars.

Related Experiment Videos

  • Development of new approaches extending established principles.

    • Main Results:

    • Nearly all methods for modeling RNA and protein structure are based on the same core principles.
    • These diverse methods can be converted into equivalent approaches using tree-adjoining grammars.
    • New methods are proposed that extend these core principles in novel ways.

    Conclusions:

    • A unified framework based on tree-adjoining grammars can encompass most existing computational approaches to RNA and protein structure.
    • This unification facilitates understanding and potentially improves the development of new modeling techniques.
    • The proposed extensions offer novel avenues for future research in structural bioinformatics.