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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...

Conservation of Protein Domains

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Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

Protein Complexes with Interchangeable Parts

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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.
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Protein Organization

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Related Experiment Video

Updated: Nov 27, 2025

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

Residue Cluster Classes: A Unified Protein Representation for Efficient Structural and Functional Classification.

Fernando Fontove¹, Gabriel Del Rio²

¹C3 Consensus, Miguel Hidalgo, CDMX, Mexico City 11510, Mexico.

Entropy (Basel, Switzerland)

|December 8, 2020

Summary

This summary is machine-generated.

This study introduces residue cluster classes (RCCs), a unified protein representation derived from 3D structures. This method enables effective protein structure and function classification using random forest algorithms.

Keywords:

functional classification residue cluster class structural classification

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Last Updated: Nov 27, 2025

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

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Published on: July 14, 2015

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Published on: July 12, 2022

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Computational Biology
Structural Bioinformatics
Protein Science

Background:

Protein structure and function are intrinsically linked, yet distinct computational models are typically used for each.
Developing a unified representation for both protein structure and function is a significant challenge in bioinformatics.

Purpose of the Study:

To develop a computationally efficient method for generating a unified protein representation.
To demonstrate the effectiveness of this representation in classifying both protein structure and function.

Main Methods:

Calculation of residue cluster classes (RCCs) from protein 3D structures.
Generation of residue contact maps using various distance criteria (7-8 Å, with/without side-chain atoms).
Application of a random forest algorithm for classification tasks.

Main Results:

Residue cluster classes (RCCs) provide an effective unified representation for proteins.
The random forest model achieved successful classification of protein structures (CATH) and functions (Gene Ontology).
Optimal classification performance was observed using distance criteria of 7 or 8 Å.

Conclusions:

A unified protein representation (RCCs) can effectively model both structural and functional aspects of proteins.
This approach offers a computationally efficient solution for large-scale protein analysis.
Future work can explore further refinements and applications of this unified representation.