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

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...

Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

From DNA to Protein

From DNA to Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

Proteins: From Genes to Degradation

Proteins: From Genes to Degradation

Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick. Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
Transcription is the synthesis of RNA...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

The Central Dogma

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between DNA and Proteins
In the early 1900s, scientists discovered that DNA stores all the information needed for cellular functions and that proteins perform most of these functions. However, the mechanisms of converting genetic information into functional proteins remained unknown for many years. Initially, it was believed that a single gene is...

You might also read

Related Articles

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

Sort by

Same author

Efficient generation of epitope-targeted antibodies with Germinal.

Nature biotechnology·2026

Same author

iNOS modulates inflammatory responses in an NO-independent manner through direct interaction with IRG1 in mitochondria.

Nature metabolism·2026

Same author

Rational discovery of therapeutic PAK1 allosteric activators.

Cell·2026

Same author

Genome modelling and design across all domains of life with Evo 2.

Nature·2026

Same author

Rapid directed evolution guided by protein language models and epistatic interactions.

Science (New York, N.Y.)·2026

Same author

Sidechain conditioning and modeling for full-atom protein sequence design with FAMPNN.

Proceedings of machine learning research·2025

Search research articles

Related Experiment Video

Updated: Jun 27, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Generative artificial intelligence for de novo protein design.

Adam Winnifrith¹, Carlos Outeiral², Brian L Hie³

¹Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, United Kingdom; Evolvere Biosciences, Innovation Building, Old Road Campus, Oxford, OX3 7FZ, United Kingdom.

Current Opinion in Structural Biology

|April 25, 2024

Summary

Artificial intelligence is revolutionizing de novo protein design, enabling the creation of novel proteins with specific functions. This review offers a framework for understanding these AI tools and their integration into protein engineering workflows.

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

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 27, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

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:

Biochemistry
Computational Biology
Protein Engineering

Background:

Protein engineering aims to create novel molecules beyond natural evolution.
Artificial intelligence (AI) advancements, particularly generative models, are accelerating de novo protein design.
Current AI-driven design protocols show experimental success rates approaching 20%.

Purpose of the Study:

To provide a framework for understanding the role of AI tools in de novo protein design.
To highlight challenges and opportunities in AI-assisted protein engineering.
To emphasize the importance of integrating biochemical knowledge into AI design processes.

Main Methods:

Review of current AI architectures (e.g., language models, diffusion processes) for protein generation.
Analysis of state-of-the-art de novo protein design protocols.
Discussion of in silico metrics for design prioritization and experimental validation.

Main Results:

AI models demonstrate capability in generating realistic and functional novel proteins.
Experimental success rates for de novo designed proteins are improving.
Key challenges remain in optimizing design prioritization and engineering complex protein behaviors.

Conclusions:

AI significantly enhances the de novo design of proteins with desired functions.
Integrating biochemical knowledge is crucial for improving AI model performance and interpretability.
Further research is needed to address challenges in designing proteins with complex conformational changes and post-translational modifications.