Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

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...

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

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...

Mechanical Protein Function

Mechanical Protein Function

You might also read

Related Articles

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

Sort by

Same author

The structure-function relationships and physiological roles of MnSOD mutants.

Bioscience reports·2022

Same author

Automated segmentation of microtomography imaging of Egyptian mummies.

PloS one·2021

Same author

Substitution of histidine 30 by asparagine in manganese superoxide dismutase alters biophysical properties and supports proliferation in a K562 leukemia cell line.

European biophysics journal : EBJ·2021

Same author

Potential Therapeutic Applications of MnSODs and SOD-Mimetics.

Chemistry (Weinheim an der Bergstrasse, Germany)·2017

Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026

Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026

Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026

Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026

Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026

Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 5, 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

Machine learning techniques for protein function prediction.

Rosalin Bonetta¹, Gianluca Valentino²

¹Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta.

|October 12, 2019

Summary

This summary is machine-generated.

Computational methods are crucial for predicting protein function due to experimental limitations. This review covers machine learning techniques and feature engineering advancements for accurate protein function prediction.

Keywords:

deep learning feature selection machine learning protein function prediction

More Related Videos

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

Related Experiment Videos

Last Updated: Jan 5, 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

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

Area of Science:

Proteomics and Bioinformatics
Computational Biology
Machine Learning in Biology

Background:

Protein structure dictates function, but experimental characterization lags behind discovery.
Predicting protein function computationally is essential due to experimental limitations.

Purpose of the Study:

To review machine learning techniques for protein function prediction.
To explore the evolution of features used in these prediction models.

Main Methods:

Review of machine learning algorithms (logistic regression, SVMs, deep neural networks).
Analysis of feature engineering: physicochemical properties, amino acid composition, text-derived features, autoencoders.
Discussion of hyperparameter optimization, feature selection, and dimensionality reduction.

Main Results:

Machine learning models have advanced significantly for protein function prediction.
Feature representations have evolved from basic properties to complex learned representations.
Successes in both general and specific protein function prediction are documented.

Conclusions:

Machine learning offers powerful tools for deciphering protein functions.
The integration of diverse features enhances prediction accuracy.
Continued development in computational approaches is vital for biological discovery.