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

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

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...

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

mRNA Stability and Gene Expression

mRNA Stability and Gene Expression

The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
Cis-acting Elements involved in mRNA stability

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...

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....

You might also read

Related Articles

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

Sort by

Same author

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026

Same author

The elusive genomic signature of tadpole shrimps' ancient morphology.

Biology letters·2026

Same author

<i>Acinetobacter</i> enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.

mSphere·2026

Same author

A genome-annotated bacterial collection of the plant food system microbiota.

Microbiology resource announcements·2025

Same author

DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology.

GigaScience·2024

Same author

Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length.

Molecules (Basel, Switzerland)·2024

Search research articles

Related Experiment Video

Updated: Jun 3, 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

DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep

Castrense Savojardo¹, Matteo Manfredi¹, Pier Luigi Martelli¹

¹Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Via San Giacomo 9/2, Bologna, 40126, Italy.

Bioinformatics (Oxford, England)

|January 12, 2025

Summary

Predicting protein stability changes from residue variations is crucial for protein design and disease research. A new method, DDGemb, uses protein language models and transformers to accurately predict these changes for single and multiple variations.

More Related Videos

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

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

Related Experiment Videos

Last Updated: Jun 3, 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

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

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

Area of Science:

Computational biology
Protein engineering
Bioinformatics

Background:

Understanding protein stability changes due to residue variations is vital for protein design and disease research.
Computational methods offer efficient screening of numerous protein variations.

Purpose of the Study:

To introduce DDGemb, a novel computational method for predicting protein stability changes (ΔΔG) upon residue variations.
To evaluate DDGemb's performance on single- and multi-point variations.

Main Methods:

DDGemb integrates protein language model embeddings with transformer architectures.
The method was trained on a curated dataset and validated using benchmark datasets.

Main Results:

DDGemb achieves state-of-the-art performance in predicting ΔΔG for both single- and multi-point variations.
The method demonstrates high accuracy across diverse datasets.

Conclusions:

DDGemb provides a powerful tool for predicting the impact of protein variations on stability.
The method advances computational approaches in protein engineering and disease variant analysis.