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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 form...
Protein Networks02:26

Protein Networks

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,...
Subcellular Fractionation01:32

Subcellular Fractionation

The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...
Membrane Domains01:18

Membrane Domains

The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the anterior...

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Related Experiment Video

Updated: Jul 15, 2026

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach
04:25

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach

Published on: August 8, 2025

Prediction of subcellular protein localization based on functional domain composition.

Peilin Jia1, Ziliang Qian, Zhenbin Zeng

  • 1Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China. pljia@sibs.ac.cn

Biochemical and Biophysical Research Communications
|April 13, 2007
PubMed
Summary

This study introduces a machine learning system using the Nearest Neighbor Algorithm (NNA) to predict protein subcellular localization (SL) with 93.96% accuracy. This computational approach offers an efficient alternative to experimental methods for large-scale protein analysis.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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Last Updated: Jul 15, 2026

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach
04:25

Enriching Subcellular Proteins in Leptospira Using a Triton X-114-Based Fractionation Approach

Published on: August 8, 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

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Determining protein subcellular localization (SL) is crucial for functional proteomics.
  • Experimental methods for SL determination are time-consuming and not high-throughput.
  • Computational prediction is preferred for large-scale SL assignment.

Purpose of the Study:

  • To develop an accurate and efficient computational system for predicting protein subcellular localization (SL).
  • To incorporate protein functional domain profiles into a machine learning model for enhanced prediction accuracy.

Main Methods:

  • Utilized the Nearest Neighbor Algorithm (NNA), a machine learning approach.
  • Incorporated protein functional domain profiles into the prediction model.
  • Developed the Subcellular Location Prediction System (SLPS).

Main Results:

  • Achieved an overall prediction accuracy of 93.96%.
  • Demonstrated the system's validity and efficiency through comparisons with other methods.
  • Provided an accessible online implementation of the prediction system.

Conclusions:

  • The developed NNA-based system provides a highly accurate computational method for protein SL prediction.
  • The system offers a valuable tool for large-scale functional proteomics research.
  • The Subcellular Location Prediction System (SLPS) is available online for broader scientific use.