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-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...

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...

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....

You might also read

Related Articles

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

Sort by

Same author

UTag, a cysteine-free thermostable tagging system for tracking single mRNA translation live.

Research square·2026

Same author

UTag, a cysteine-free thermostable tagging system for tracking single mRNA translation live.

bioRxiv : the preprint server for biology·2026

Same author

Efficiency Enhancement and Transparency Adaption of Bladed PM6:Y6 Solar Cells Doped with Binary Lanthanide (Eu<sup>3+</sup>/Sm<sup>3+</sup>)-Induced Polymeric Nanoaggregates.

ACS applied materials & interfaces·2026

Same author

Eu<sup>3+</sup> Complex-Protein Co-Crystals as Smart Sensors of Biologically Relevant Cations in Blood.

Materials (Basel, Switzerland)·2026

Same author

Modular Scaffold Crystals for Programmable Installation and Structural Observation of DNA-Binding Proteins.

bioRxiv : the preprint server for biology·2026

Same author

AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications.

Science advances·2026

Same journal

Nanotechnology-Stem Cell Strategies in 3D Glioblastoma Organoid: Targeting Glioma Stem Cells Within a Complex Tumor Microenvironment.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 24, 2026

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

Methods for library-scale computational protein design.

Lucas B Johnson¹, Thaddaus R Huber, Christopher D Snow

¹Department of Chemical and Biological Engineering, Colorado State University, 356 Scott Bioengineering, 1301 Campus Delivery, Fort Collins, CO, 80523-1301, USA.

Methods in Molecular Biology (Clifton, N.J.)

|September 13, 2014

Summary

This summary is machine-generated.

Library-scale computational protein design (LCPD) offers a hybrid approach for engineering diverse protein variants. This method presents practical techniques for both delocalized and localized protein design challenges.

More Related Videos

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

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

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

Published on: January 26, 2024

Related Experiment Videos

Last Updated: Apr 24, 2026

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

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

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

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

Published on: January 26, 2024

Area of Science:

Biochemistry
Computational Biology
Protein Engineering

Background:

Protein engineering presents complex design challenges for researchers.
Library-scale computational protein design (LCPD) is a hybrid strategy for creating improved protein variants with diverse sequences.

Purpose of the Study:

To discuss the background and merits of practical LCPD techniques.
To illustrate LCPD methods using specific examples in protein engineering.

Main Methods:

Presentation of LCPD methods for delocalized protein design.
Discussion of localized design methods for targeted protein modifications.

Main Results:

Example design calculations for cellobiohydrolase II using delocalized LCPD.
Example design calculation for shifting ketol-acid reductoisomerase substrate specificity from NADPH to NADH using localized LCPD.

Conclusions:

LCPD provides a versatile framework for addressing diverse protein engineering objectives.
The discussed techniques offer practical approaches for designing novel protein functions and properties.