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

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

14.7K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
14.7K
Mechanical Protein Functions01:58

Mechanical Protein Functions

5.7K
Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force. 
5.7K
Conservation of Protein Domains02:26

Conservation of Protein Domains

4.2K
4.2K
Affinity and Avidity01:41

Affinity and Avidity

39.3K
Overview
39.3K
Electron Affinity03:07

Electron Affinity

43.7K
The electron affinity (EA) is the energy change for adding an electron to a gaseous atom to form an anion (negative ion).
43.7K
Structural Protein Function01:56

Structural Protein Function

30.1K
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to...
30.1K

You might also read

Related Articles

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

Sort by
Same author

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same author

Multidimensional Dysfunction in Chronic Nonspecific Low Back Pain: A Correlational Study of Key Clinical Measures.

Pain research & management·2026
Same author

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026
Same author

Association of the skeletal muscle mass-to-visceral fat area ratio with cardiovascular disease: a cross-sectional study based on NHANES.

Eating and weight disorders : EWD·2026
Same author

Differential neural responses to rhythmic motion and rhythmic static auditory stimuli: An EEG and fNIRS study.

Hearing research·2026
Same author

Explicit and implicit emotion regulation in individuals with problematic internet use: Evidence from effective connectivity.

Psychiatry research. Neuroimaging·2026

Related Experiment Video

Updated: Feb 14, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.9K

PANDA: Protein function prediction using domain architecture and affinity propagation.

Zheng Wang1, Chenguang Zhao2, Yiheng Wang2

  • 1Department of Computer Science, University of Miami, 1364 Memorial Drive, P.O. Box 248154, Coral Gables, FL, 33124, USA. zheng.wang@miami.edu.

Scientific Reports
|February 24, 2018
PubMed
Summary
This summary is machine-generated.

We developed PANDA (Propagation of Affinity and Domain Architecture) to predict protein functions using Gene Ontology (GO) terms. This novel tool outperforms existing methods in predicting protein functions.

More Related Videos

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.6K
The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis
19:16

The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis

Published on: March 17, 2010

21.2K

Related Experiment Videos

Last Updated: Feb 14, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.9K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.6K
The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis
19:16

The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis

Published on: March 17, 2010

21.2K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate prediction of protein function is crucial for understanding biological processes.
  • Existing methods for protein function prediction have limitations in accuracy and scope.

Purpose of the Study:

  • To develop a novel computational tool, PANDA (Propagation of Affinity and Domain Architecture), for predicting protein functions.
  • To improve the accuracy and reliability of protein function prediction using Gene Ontology (GO) terms.

Main Methods:

  • PANDA utilizes profile-profile alignment against protein databases (PfamA, KOG, COG, SwissProt) and PSI-BLAST against UniProt for homology searches.
  • It integrates a Bayesian statistics-based domain architecture inference algorithm to calculate GO term probabilities.
  • Candidate GO terms undergo Z-score filtering, affinity propagation clustering based on the GO directed acyclic graph, and a second filtering round.

Main Results:

  • PANDA demonstrated superior performance compared to baseline predictors.
  • The tool achieved higher area under the curve for precision and recall metrics.
  • Benchmarking confirmed the effectiveness of PANDA's pooling and filtering steps.

Conclusions:

  • PANDA is an effective tool for predicting protein functions with improved accuracy.
  • The integrated approach of domain architecture inference and affinity propagation enhances prediction reliability.
  • PANDA offers a valuable resource for the scientific community, accessible at http://dna.cs.miami.edu/PANDA/.