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Conservation of Protein Domains Over Different Proteins

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...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

Conservation of Protein Domains

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...

Conserved Binding Sites

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...

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

Protein Folding

Protein Folding

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Related Experiment Video

Updated: Jun 10, 2026

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

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

Published on: July 14, 2015

Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support

Khader Shameer¹, Ganesan Pugalenthi, Krishna Kumar Kandaswamy

¹National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, 560065, India.

Bioinformatics and Biology Insights

|July 17, 2010

Summary

This summary is machine-generated.

We developed a machine learning model to predict protein 3-dimensional domain swapping, a process implicated in neurodegenerative diseases. This computational tool aids in identifying proteins prone to this structural change.

Keywords:

3D domain swapping SVM domain swap feature selection machine learning

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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Last Updated: Jun 10, 2026

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

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

Published on: July 14, 2015

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

Structural biology
Computational biology
Biochemistry

Background:

3-dimensional domain swapping involves protein subunits exchanging identical or similar parts to form oligomers.
This phenomenon is increasingly linked to prions and neurodegenerative diseases, affecting protein function, aggregation, and misfolding.
Identifying common sequence or structural patterns in swapped proteins is challenging despite structural analysis capabilities.

Purpose of the Study:

To develop a computational method for predicting 3-dimensional domain swapping events.
To utilize sequence and structural data for building a predictive classifier.
To facilitate the identification of novel proteins involved in domain swapping and related deposition diseases.

Main Methods:

A Support Vector Machine (SVM)-based classifier was developed.
The classifier was trained using features derived from sequence and structural data of 150 known 3D domain-swapping proteins and 150 non-swapping proteins.
Performance was evaluated using a separate test set of 63 swapping and 63 non-swapping proteins.

Main Results:

The SVM classifier achieved 76.33% accuracy during training.
The model demonstrated 73.81% accuracy on the independent testing dataset.
Feature selection identified key sequence and structure-derived features relevant to the domain swapping mechanism.

Conclusions:

The developed SVM classifier provides a valuable tool for predicting 3D domain swapping events.
This algorithm represents an initial step towards identifying more proteins potentially involved in swapping and deposition diseases.
Further analysis of identified features can enhance understanding of the 3D domain swapping mechanism.