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 Folding01:25

Protein Folding

9.7K
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...
9.7K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.3K
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...
13.3K
Protein and Protein Structure02:15

Protein and Protein Structure

83.5K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
83.5K
Protein and Protein Structures02:15

Protein and Protein Structures

14.1K
14.1K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.4K
3.4K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.7K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.7K

You might also read

Related Articles

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

Sort by
Same author

VDR/RXR antagonizes calcineurin-activated NFAT1, an essential regulator of Coronin-1A expression and Mycobacterial persistence.

The Biochemical journal·2026
Same author

Self-healing chitosan-catechol hydrogel with tailored self-assembled fibrillar or micellar structures for biomedical applications.

Carbohydrate polymers·2026
Same author

Building MCP-native hierarchical AI scientist ecosystems: a perspective on scaling multi-agent scientific discovery.

Frontiers in artificial intelligence·2026
Same author

Biomechanical effects of various occlusal conditions and orthodontic force levels on mandibular canine distalization: a finite element analysis.

Scientific reports·2026
Same author

Enhanced Hypoglycemic Activity of Metformin with the Reduction of the Particle Size.

Biotechnology and applied biochemistry·2026
Same author

Blue-Light-Free Orange-Red Organic Light-Emitting Diodes With Less Influence on Melatonin Secretion.

Small (Weinheim an der Bergstrasse, Germany)·2026
Same journal

What do LLMs value? An evaluation framework for revealing subjective trade-offs in assessment of glycemic control.

Proceedings of machine learning research·2026
Same journal

Towards the Efficient Inference by Incorporating Automated Computational Phenotypes under Covariate Shift.

Proceedings of machine learning research·2026
Same journal

Endo-SemiS: Towards Robust Semi-Supervised Image Segmentation for Endoscopic Video.

Proceedings of machine learning research·2026
Same journal

Perspective: Machine Learning for Health Should Consider Social Drivers of Health.

Proceedings of machine learning research·2026
Same journal

Classifying Phonotrauma Severity from Vocal Fold Images with Soft Ordinal Regression.

Proceedings of machine learning research·2026
Same journal

Does Domain-Specific Retrieval Augmented Generation Help LLMs Answer Consumer Health Questions?

Proceedings of machine learning research·2026
See all related articles

Related Experiment Video

Updated: Oct 23, 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

Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design.

Yue Cao1,2, Payel Das1, Vijil Chenthamarakshan1

  • 1IBM Research.

Proceedings of Machine Learning Research
|August 23, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces Fold2Seq, a new AI framework for designing protein sequences based on their 3D structure. Fold2Seq effectively generates diverse and reliable protein sequences for specific folds, outperforming existing methods.

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

482
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.4K

Related Experiment Videos

Last Updated: Oct 23, 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

482
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.4K

Area of Science:

  • Protein Engineering
  • Computational Biology
  • Bioinformatics

Background:

  • Designing protein sequences for specific 3D folds is challenging due to complex sequence-structure relationships.
  • Existing methods struggle to capture sequence diversity within a given fold.

Purpose of the Study:

  • To develop a novel generative framework, Fold2Seq, for designing protein sequences conditioned on a target 3D fold.
  • To improve the speed, coverage, and reliability of protein sequence design.

Main Methods:

  • Fold2Seq utilizes a transformer-based architecture for sequence and fold embedding.
  • It models the sequence-structure relationship by learning from secondary structural element densities in 3D voxels.

Main Results:

  • Fold2Seq demonstrates comparable or improved performance in speed, coverage, and reliability against state-of-the-art methods.
  • The framework shows particular advantages when dealing with low-quality, incomplete, or ambiguous input structures.

Conclusions:

  • Fold2Seq offers a powerful and versatile approach for protein sequence design based on topological folds.
  • The method advances the field of protein engineering by enabling more robust sequence generation for desired structures.