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

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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-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...

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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....

Protein-Protein Interfaces

Protein-Protein Interfaces

You might also read

Related Articles

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

Sort by

Same author

Sublytic C5b-9 triggers glomerular mesangial cell apoptosis in rat Thy-1 nephritis via Gadd45 activation mediated by Egr-1 and p300-dependent ATF3 acetylation.

Journal of molecular cell biology·2016

Same author

Improving the hydrogen selectivity of graphene oxide membranes by reducing non-selective pores with intergrown ZIF-8 crystals.

Chemical communications (Cambridge, England)·2016

Same author

The Association Between Genetic Polymorphism rs703842 in CYP27B1 and Multiple Sclerosis: A Meta-Analysis.

Medicine·2016

Same author

High-Flexibility, High-Toughness Double-Cross-Linked Chitin Hydrogels by Sequential Chemical and Physical Cross-Linkings.

Advanced materials (Deerfield Beach, Fla.)·2016

Same author

Synthesis, structure, and magnetic and catalytic properties of metal frameworks with 2,2'-dinitro-4,4'-biphenyldicarboxylate and imidazole-containing tripodal ligands.

Dalton transactions (Cambridge, England : 2003)·2016

Same author

Reactive oxygen species and hormone signaling cascades in endophytic bacterium induced essential oil accumulation in Atractylodes lancea.

Planta·2016

Search research articles

Related Experiment Video

Updated: Jul 20, 2025

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

PocketAnchor: Learning structure-based pocket representations for protein-ligand interaction prediction.

Shuya Li¹, Tingzhong Tian¹, Ziting Zhang²

¹Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China.

|July 29, 2023

Summary

PocketAnchor is a new method for representing protein pockets to improve predictions of protein-ligand interactions. This structure-based approach effectively captures pocket features, aiding drug discovery.

Keywords:

binding affinity prediction pocket detection protein structural representation protein-ligand interaction

More Related Videos

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

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: Jul 20, 2025

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

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

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Computational biology
Structural bioinformatics
Drug discovery

Background:

Protein-ligand interactions are crucial for biological processes and drug development.
Accurate computational prediction of these interactions requires effective protein feature representation.
Existing methods may not fully capture the characteristics of protein pockets relevant to ligand binding.

Purpose of the Study:

To develop a novel structure-based protein representation method, PocketAnchor.
To capture local environmental and spatial features of protein pockets.
To enhance computational prediction of protein-ligand interactions.

Main Methods:

Defined "anchors" as probe points within protein cavities and near surfaces.
Developed a message-passing strategy to aggregate information from atoms and surfaces around anchors.
Applied PocketAnchor to pocket detection and binding affinity prediction tasks.

Main Results:

PocketAnchor successfully captured local pocket features.
The method demonstrated effectiveness in pocket detection.
PocketAnchor improved binding affinity prediction accuracy.

Conclusions:

The anchor-based approach provides effective protein feature representations.
PocketAnchor enhances the prediction of protein-ligand interactions.
This method holds promise for advancing computational drug discovery.