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 Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

5.4K
Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
5.4K
Protein Organization01:24

Protein Organization

9.0K
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....
9.0K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

14.0K
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...
14.0K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

19.2K
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...
19.2K
Protein Folding01:25

Protein Folding

10.9K
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...
10.9K

You might also read

Related Articles

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

Sort by
Same author

Precision-guided immunomodulatory therapy in sepsis.

The Lancet. Respiratory medicine·2026
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

Effects of a Combined Dietary and Physical Activity Intervention on Bone Density, Lean Mass and Fat Mass in Adults: The GOTO Trial.

Journal of cachexia, sarcopenia and muscle·2026
Same author

Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.

Genome biology·2026
Same author

Domain mapping of disease mutations reveals pathogenic SORL1 variants in Alzheimer's disease.

Molecular neurodegeneration·2025
Same author

Work smarter, not harder: achieve expert-level diagnosis extraction from medical records with optimal prompting of large language models.

Annals of the rheumatic diseases·2025
Same journal

Computational design of low-volatility lubricants for space using interpretable machine learning.

Journal of cheminformatics·2026
Same journal

OpenStats: how to combine statistics and research data management (RDM) to leverage efficient scientific data analysis by guided statistics.

Journal of cheminformatics·2026
Same journal

Unified heterogeneity-aware benchmark of drug synergy prediction: a cross-study analysis of traditional machine learning and graph deep learning models.

Journal of cheminformatics·2026
Same journal

Count your bits: fingerprint benchmarking to assess broad chemical space representation.

Journal of cheminformatics·2026
Same journal

Sampling out-of-distribution chemical spaces via Bayesian flow.

Journal of cheminformatics·2026
Same journal

Hold on tight: the kinetic profiling of opioid receptor ligands using the CORAL-MD.

Journal of cheminformatics·2026
See all related articles

Related Experiment Video

Updated: Jan 9, 2026

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

17.5K

All-atom protein sequence design using discrete diffusion models.

Amelia Villegas-Morcillo1, Gijs J Admiraal1, Marcel J T Reinders1

  • 1Department of Intelligent Systems, Delft University of Technology, Delft , The Netherlands.

Journal of Cheminformatics
|December 2, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces an all-atom protein sequence generation method using SELFIES, enhancing novelty and diversity in protein design. While challenges remain in generating valid proteins, this approach offers broader possibilities beyond traditional amino acid sequences.

Keywords:
All-atom representationDiscrete diffusion modelsGenerative modelingProtein sequence design

More Related Videos

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.5K
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

903

Related Experiment Videos

Last Updated: Jan 9, 2026

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

17.5K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.5K
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

903

Area of Science:

  • Computational biology
  • Protein engineering
  • Artificial intelligence in drug discovery

Background:

  • Traditional protein sequence representation limits the inclusion of non-canonical amino acids and post-translational modifications.
  • Advancing protein design is key for breakthroughs in medicine and biotechnology.

Purpose of the Study:

  • To explore discrete diffusion models for novel protein sequence generation using an all-atom chemical representation (SELFIES).
  • To evaluate the impact of all-atom representation on protein quality, diversity, and novelty compared to amino acid-based models.
  • To assess the effectiveness of different noise schedules (uniform vs. absorbing) in the diffusion process.

Main Methods:

  • Utilized a modified ByteNet architecture within the discrete diffusion D3PM framework.
  • Employed the SELFIES (SMILES-like) all-atom chemical representation for protein sequences.
  • Developed a comprehensive assessment pipeline to validate generated protein sequences for canonical and non-canonical amino acid content.
  • Compared generation performance using uniform and absorbing noise schedules.

Main Results:

  • Models using all-atom representation generated proteins with improved novelty and diversity compared to amino acid-based models.
  • Successfully generated proteins using the all-atom approach demonstrated comparable structural foldability.
  • The all-atom representation faced challenges in consistently generating fully valid protein sequences.
  • The absorbing noise schedule proved most effective for both all-atom and amino acid-based representations.

Conclusions:

  • The all-atom SELFIES representation shows promise for enhancing novelty and diversity in protein sequence generation.
  • Further refinement is needed to ensure consistent generation of valid protein structures with non-canonical elements.
  • The absorbing noise schedule is recommended for optimizing discrete diffusion models in protein sequence generation.