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 Organization

Protein Organization

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.

Conserved Binding Sites

Conserved Binding Sites

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 analyses the...

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

Protein Folding

Protein Folding

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...

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 can...

Protein-protein Interfaces

Protein-protein Interfaces

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 polypeptide...

You might also read

Related Articles

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

Sort by

Same author

Trefoil polymers from a knotted synthon.

Nature chemistry·2026

Same author

Generating knotted polymer and protein structures by machine learning.

Communications chemistry·2026

Same author

A framework for building a synthetic cell from the SynCell Asia Initiative.

Nature biotechnology·2026

Same author

Preparation of Nanostructured FeCoNiMgO<sub><i>x</i></sub> Medium-Entropy Oxides by Using a Milk Template for Efficiently Promoting Oxygen Evolution Reaction.

Langmuir : the ACS journal of surfaces and colloids·2026

Same author

Lingguizhugan Decoction Ameliorates MASLD by Modulating the Gut Microbiota and Enriching Non-12-OH Bile Acids to Activate TGR5-Mediated Thermogenesis.

Pharmaceuticals (Basel, Switzerland)·2026

Same author

The scientific legacy of Martin Karplus from the perspective of his collaborators.

Biophysical journal·2026

Search research articles

Related Experiment Video

Updated: Jun 12, 2026

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

Improving computational protein design by using structure-derived sequence profile.

Liang Dai¹, Yuedong Yang, Hyung Rae Kim

¹School of Informatics, Indiana University Purdue University, Indianapolis, Indiana 46202, USA.

|June 15, 2010

Summary

This summary is machine-generated.

This study introduces RosettaDesign-SR, a new computational method for protein design. It improves sequence identity to wild-type proteins and increases polar residues, potentially reducing aggregation and enhancing structural uniqueness.

More Related Videos

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

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Related Experiment Videos

Last Updated: Jun 12, 2026

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

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

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

Protein Engineering
Computational Biology
Biochemistry

Background:

Designing protein sequences for specific structures is crucial for both practical applications and fundamental understanding.
Previous methods focused on side-chain interactions, but the link between backbone structure and local sequence remains a challenge.

Purpose of the Study:

To develop a novel computational method that accounts for main-chain backbone structure and local sequence coupling in protein design.
To improve the accuracy and relevance of designed protein sequences compared to existing methods.

Main Methods:

Implemented a sequence profile from structurally matched five-residue fragments.
Introduced a term to minimize low-complexity regions in designed sequences.
Integrated these features into the RosettaDesign program, creating RosettaDesign-SR.

Main Results:

Achieved a 12% increase in designed sequences with >35% identity to wild-type sequences (34% to 46%).
Reduced non-homologous designed sequences by 8% (22% to 14%) as per psi-blast.
Observed a 2-3% increase in polar residues at protein surfaces and cores, with 4% higher wild-type sequence identity.

Conclusions:

RosettaDesign-SR enhances protein design by better integrating backbone and sequence information.
The method leads to designed proteins with improved sequence identity and increased surface/core polarity.
These improvements suggest designed proteins will be less prone to aggregation and possess more unique structures.