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 Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
Protein Networks02:26

Protein Networks

4.0K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.0K

You might also read

Related Articles

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

Sort by
Same author

Ultrastructural changes in cryopreserved tracheal grafts of sprague-dawley rats.

ASAIO journal (American Society for Artificial Internal Organs : 1992)Ā·2009
Same author

Facile synthesis of size-tunable micro-octahedra via metal-organic coordination.

Chemical communications (Cambridge, England)Ā·2009
Same author

N-acetyl cysteine and penicillamine induce apoptosis via the ER stress response-signaling pathway.

Molecular carcinogenesisĀ·2009
Same author

Targeting glucosylceramide synthase downregulates expression of the multidrug resistance gene MDR1 and sensitizes breast carcinoma cells to anticancer drugs.

Breast cancer research and treatmentĀ·2009
Same author

N-glycosylation of ATF6beta is essential for its proteolytic cleavage and transcriptional repressor function to ATF6alpha.

Journal of cellular biochemistryĀ·2009
Same author

A humanized anti-osteopontin antibody inhibits breast cancer growth and metastasis in vivo.

Cancer immunology, immunotherapy : CIIĀ·2009

Related Experiment Video

Updated: Jul 11, 2025

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
07:24

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

2.4K

LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm.

Minzhu Xie1, Ruijie Xie1, Hao Wang1

  • 1College of Information Science and Engineering, Hunan Normal University, China.

Methods (San Diego, Calif.)
|November 16, 2023
PubMed
Summary

Predicting long-chain noncoding RNA (lncRNA)-protein interactions is key to understanding lncRNA function. The LPI-IBWA model effectively predicts these interactions using integrated biological data and advanced algorithms, achieving high accuracy.

Keywords:
ProteinSimilarity kernel fusionWeighted k-nearest known neighborslncRNAlncRNA-protein interactions

More Related Videos

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
10:45

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

58.5K
Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

8.2K

Related Experiment Videos

Last Updated: Jul 11, 2025

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
07:24

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

2.4K
iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
10:45

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

58.5K
Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

8.2K

Area of Science:

  • Computational biology
  • Bioinformatics
  • Genomics

Background:

  • Long-chain noncoding RNAs (lncRNAs) regulate gene expression through protein interactions.
  • Understanding lncRNA function requires accurate prediction of these interactions.
  • Existing methods for predicting lncRNA-protein interactions have limitations.

Purpose of the Study:

  • To develop a novel computational model, LPI-IBWA, for predicting lncRNA-protein interactions.
  • To improve the accuracy and efficiency of lncRNA-protein interaction prediction.
  • To infer the functions of lncRNAs through interaction prediction.

Main Methods:

  • Similarity Kernel Fusion (SKF) to integrate diverse biological data and construct similarity networks.
  • Bounded matrix completion and weighted k-nearest known neighbors algorithm to update the interaction matrix.
  • Improved Bi-Random walk algorithm for predicting latent lncRNA-protein interactions within a heterogeneous network.

Main Results:

  • LPI-IBWA achieved high performance with AUC of 0.920 and AUPR of 0.736 on a benchmark dataset.
  • The model outperformed existing state-of-the-art methods in predicting lncRNA-protein interactions.
  • Case studies demonstrated LPI-IBWA's efficiency in identifying potential novel interactions.

Conclusions:

  • LPI-IBWA is an effective computational tool for predicting lncRNA-protein interactions.
  • The model's accuracy facilitates the inference of lncRNA functions.
  • This approach advances the field of lncRNA research and functional genomics.