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

Protein Diffusion in the Membrane

Protein Diffusion in the Membrane

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...

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 Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

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...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Protein and Protein Structure

Protein and Protein Structure

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...

Protein and Protein Structures

Protein and Protein Structures

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

ST-PARM: Pareto-Complete Inference-Time Alignment for Multi-Objective Protein Design.

bioRxiv : the preprint server for biology·2026

Same author

Current and future directions in network biology.

Bioinformatics advances·2024

Same author

Novel antibody language model accelerates IgG screening and design for broad-spectrum antiviral therapy.

bioRxiv : the preprint server for biology·2024

Same author

Predicting protein structure from single sequences.

Nature computational science·2024

Same author

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

Proteins·2023

Search research articles

Related Experiment Video

Updated: Jan 11, 2026

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

Multimodal diffusion for joint design of protein sequence and structure.

Shaowen Zhu¹, Siddhant Gulati², Yuxuan Liu¹

¹Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA.

Protein Science : a Publication of the Protein Society

|November 14, 2025

Summary

This summary is machine-generated.

This study presents a new computational method for designing protein sequences and structures together, enabling faster and more functional protein creation. Experimental results show promising functional protein designs, accelerating future applications.

Keywords:

diffusion models generative models machine learning protein design

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

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

Related Experiment Videos

Last Updated: Jan 11, 2026

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

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

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

Area of Science:

Protein Engineering
Computational Biology
Structural Biology

Background:

Designing functional proteins computationally is crucial for both basic science and practical applications.
Existing methods often design protein sequence and structure in separate stages, which can be inefficient.

Purpose of the Study:

To develop a unified generative framework for co-designing protein sequence and structure simultaneously.
To enable cross-modality interactions for coherent and functional protein designs.

Main Methods:

A generative framework modeling the joint distribution of protein sequence and structure.
Representing residues using three modalities: type, position, and orientation, each modeled by diffusion processes.
A unified architecture, ReverseNet, with a graph attention encoder and separate projectors for multimodal integration.

Main Results:

The proposed models (JointDiff and JointDiff-x) achieve comparable or better designability for monomer structures than two-stage models.
Models are 1-2 orders of magnitude faster, supporting rapid iterative design.
Experimental validation on green fluorescent protein (GFP) designs yielded novel, functional variants with measurable fluorescence.

Conclusions:

Joint sequence-structure generation is feasible and can accelerate functional protein design.
The framework provides a foundation for future advancements in computational protein engineering.
Open-source code and models are available for further research and application.