Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

14.1K
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...
14.1K
Conserved Binding Sites01:49

Conserved Binding Sites

4.7K
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...
4.7K
Protein Organization01:24

Protein Organization

8.2K
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....
8.2K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.5K
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...
13.5K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

18.7K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
18.7K
Protein Networks02:26

Protein Networks

4.2K
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,...
4.2K

You might also read

Related Articles

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

Sort by
Same author

Multiomic screening platform uncovers the impact of histone mutations on chromatin and cell fate.

bioRxiv : the preprint server for biology·2026
Same author

Beyond native sequence recovery: Improved modeling of the sequence-energy landscape of protein structures.

bioRxiv : the preprint server for biology·2026
Same author

A proteome-wide biochemical screen defines binding determinants of the core autophagy protein LC3B.

bioRxiv : the preprint server for biology·2026
Same author

Design of Specific Peptide Inhibitors of Toxin-Antitoxin-Mediated Antiphage Defense.

ACS synthetic biology·2025
Same author

Training bias and sequence alignments shape protein-peptide docking by AlphaFold and related methods.

Protein science : a publication of the Protein Society·2025
Same author

Jointly Embedding Protein Structures and Sequences through Residue Level Alignment.

PRX life·2025
Same journal

Tomogram exploration through template matching and deep learning.

Current opinion in structural biology·2026
Same journal

A comparative review of cryo-electron ptychography: Biological applications and future perspectives.

Current opinion in structural biology·2026
Same journal

Metabolic disruptions through a three-dimensional genomic lens.

Current opinion in structural biology·2026
Same journal

Collective variable design for biomolecular conformational dynamics.

Current opinion in structural biology·2026
Same journal

Polymer scaling in protein crowding: From dilute coils to semidilute meshes.

Current opinion in structural biology·2026
Same journal

Tuning the physicochemical properties of rationally designed protein-based biomolecular condensates.

Current opinion in structural biology·2026
See all related articles

Related Experiment Video

Updated: Nov 7, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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

Published on: July 25, 2013

17.2K

Data-driven computational protein design.

Vincent Frappier1, Amy E Keating2

  • 1Generate Biomedicines, 26 Landsdowne Street, Cambridge, MA, 02139, USA.

Current Opinion in Structural Biology
|April 28, 2021
PubMed
Summary
This summary is machine-generated.

Computational protein design creates novel proteins using existing biological data. Deep learning and advanced computational methods are key to maximizing data value for future protein engineering success.

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

551
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

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

Published on: January 26, 2024

2.2K

Related Experiment Videos

Last Updated: Nov 7, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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

Published on: July 25, 2013

17.2K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

551
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

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

Published on: January 26, 2024

2.2K

Area of Science:

  • Biochemistry
  • Computational Biology
  • Protein Engineering

Background:

  • Proteins with novel structures and functions can be generated computationally.
  • Ab initio protein design is theoretically possible but practically limited.
  • Current success relies on extensive data from existing protein sequences, structures, and functions.

Purpose of the Study:

  • To present innovative applications of computational methods in protein design.
  • To highlight the integration of diverse data types for enhanced design.
  • To discuss the future role of deep learning in protein engineering.

Main Methods:

  • Utilizing multiple-sequence alignments and protein structural data.
  • Employing high-throughput functional assays to guide design.
  • Developing regression models and deep neural networks for sequence generation.

Main Results:

  • Demonstrated creative uses of sequence and structure data in design.
  • Showcased enhancement of structure-based design with experimental data.
  • Developed deep learning models capable of generating novel protein sequences.

Conclusions:

  • Computational protein design is advancing rapidly through data-driven approaches.
  • Deep learning is poised to significantly enhance future protein design efforts.
  • Integrating diverse datasets is crucial for maximizing the potential of computational protein design.