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

Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.3K
Protein Families02:47

Protein Families

15.5K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
15.5K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.0K
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...
11.0K
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
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

4.5K
Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
4.5K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.1K
3.1K

You might also read

Related Articles

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

Sort by
Same author

Nutritional Interventions for Perimenopausal Anxiety and Depression Targeting Tryptophan and GABA Pathways: A Narrative Review.

Nutrients·2026
Same author

Nano-zeolite-coupled biochar-based phosphorus fertilizer enhances soil phosphorus availability and leaf phosphorus concentration in Moso bamboo forests.

Frontiers in plant science·2026
Same author

Photosensing PUF from an Intrinsically Random SnTe Memristor for Image Encryption and Recognition.

Nanomaterials (Basel, Switzerland)·2026
Same author

Novel Phenotypes of Acute Respiratory Failure and Differential Response to Awake Prone Positioning: A Multi-Cohort Study.

MedComm·2026
Same author

Arbuscular mycorrhiza provides postanthesis benefits to maximize wheat grain yield and nitrogen concentration.

The New phytologist·2026
Same author

MWCNT-supported PtRhFeCoMo high-entropy alloy nanocomposite for acetylcholinesterase-mediated turn-on colorimetric detection of trichlorfon.

Mikrochimica acta·2026

Related Experiment Video

Updated: Aug 5, 2025

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

68.8K

Fast and accurate protein function prediction from sequence through pretrained language model and homology-based

Qianmu Yuan1, Junjie Xie1, Jiancong Xie1

  • 1School of Computer Science and Engineering at Sun Yat-sen University.

Briefings in Bioinformatics
|March 25, 2023
PubMed
Summary

SPROF-GO accurately predicts protein functions using only protein sequences by leveraging language models and homology information. This sequence-based approach outperforms existing methods, aiding disease mechanism and drug target discovery.

Keywords:
label diffusionpretrained language modelprotein function predictionsequence-based

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

1.9K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.3K

Related Experiment Videos

Last Updated: Aug 5, 2025

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

68.8K
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

1.9K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.3K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate protein function prediction is crucial for understanding biological processes, disease mechanisms, and identifying drug targets.
  • Existing methods often rely on external data like protein structures or networks, which are not universally available.
  • Predicting protein function solely from amino acid sequences remains a significant challenge due to data volume and functional diversity.

Purpose of the Study:

  • To develop an accurate and efficient sequence-based protein function prediction method.
  • To overcome limitations of existing methods that require non-sequence data.
  • To provide a tool that generalizes well across different protein families and species.

Main Methods:

  • Utilized a pretrained language model to extract informative sequence embeddings.
  • Employed self-attention pooling to identify critical residues for function prediction.
  • Integrated homology information and label diffusion to account for functional relationships.
  • Developed SPROF-GO, a sequence-based alignment-free protein function predictor.

Main Results:

  • SPROF-GO significantly outperformed state-of-the-art sequence-based and network-based methods.
  • Achieved improvements of over 14.5%, 27.3%, and 10.1% in area under the precision-recall curve on three sub-ontology test sets.
  • Demonstrated strong generalization capabilities on non-homologous proteins and previously unseen species.
  • Attention mechanism visualization confirmed the model's ability to identify functionally relevant sequence domains.

Conclusions:

  • SPROF-GO offers a highly effective sequence-based approach for protein function prediction.
  • The method addresses the need for accurate predictions without requiring additional structural or network data.
  • SPROF-GO advances bioinformatics tools for biological research and drug discovery, with publicly available code and a web server.