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Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

Protein Networks

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,...

Protein Networks

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,...

Protein Families

Protein Families

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 locations, protein...

Protein Families

Protein Families

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 locations, protein...

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...

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Related Experiment Video

Updated: May 9, 2026

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

A review of protein function prediction under machine learning perspective.

Juliana S Bernardes¹, Carlos E Pedreira

¹Federal University of Rio de Janeiro UFRJ, COPPE-Engineering Graduate Program.

Recent Patents on Biotechnology

|July 16, 2013

Summary

Machine learning aids protein function prediction, a key challenge in proteomics. This review systematically categorizes and classifies machine learning methods for inferring protein functions, addressing limitations of traditional homology-based approaches.

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Last Updated: May 9, 2026

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:

Proteomics
Bioinformatics
Computational Biology

Background:

The exponential increase in protein identification via high-throughput techniques outpaces functional characterization.
Traditional homology-based protein function prediction methods struggle with divergent proteins.
Accurate protein function prediction requires advanced computational techniques and expressive data representation.

Purpose of the Study:

To provide a comprehensive review of machine learning (ML) approaches for protein function prediction.
To systematically categorize and classify ML methods within functional proteomics.
To highlight representative contributions and recent advancements in the field.

Main Methods:

Defining key problems in protein function understanding.
Describing the application of ML to these problems.
Categorizing and classifying existing ML methodologies.

Main Results:

A systematic framework for understanding ML's role in protein function inference.
Identification of representative ML contributions and recent advancements.
A classification of ML methods applied to functional proteomics.

Conclusions:

Machine learning offers powerful solutions to the challenges in protein function prediction.
This review provides a structured overview to navigate the rapidly evolving field of ML in proteomics.
Advanced ML techniques are crucial for accurate functional characterization of newly discovered proteins.