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...

Ligand Binding Sites

Ligand Binding Sites

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-Protein Interfaces

Protein-Protein Interfaces

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 Networks

Protein Networks

You might also read

Related Articles

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

Sort by

Same author

Mapping the Molecular Universe: Exploring Chemical Compound Space by Multiscale High-Throughput Screening and Machine Learning.

Journal of chemical information and modeling·2026

Same author

Composable free-space continuous-variable quantum key distribution using discrete modulation.

Science advances·2026

Same author

Where do we go from here? Current state of drug-target binding kinetics and a roadmap to their establishment in drug discovery campaigns.

Drug discovery today·2026

Same author

A MAFG~MITF complex drives melanoma phenotype switching and progression.

Nature communications·2026

Same author

Integrating Patient-Reported Outcome Measures in Atopic Dermatitis Clinical Practice: An Analysis of the Patient-Oriented Eczema Measure.

Pediatric dermatology·2026

Same author

Outplaying elite table tennis players with an autonomous robot.

Nature·2026

Search research articles

Related Experiment Video

Updated: Apr 20, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

LigDig: a web server for querying ligand-protein interactions.

Jonathan C Fuller¹, Michael Martinez², Stefan Henrich²

¹Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.

Bioinformatics (Oxford, England)

|December 1, 2014

Summary

LigDig is a new web server that simplifies complex queries about protein-ligand interactions. It integrates multiple data sources and tools for structure analysis, aiding researchers in drug discovery.

More Related Videos

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

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Published on: January 20, 2022

Related Experiment Videos

Last Updated: Apr 20, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 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

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Published on: January 20, 2022

Area of Science:

Bioinformatics
Computational Chemistry
Structural Biology

Background:

Protein-ligand interactions are crucial in biological processes.
Analyzing these interactions often requires multiple, disparate tools and databases.
Existing methods can be complex and time-consuming for researchers.

Purpose of the Study:

To develop a unified web server, LigDig, for analyzing protein-ligand complexes.
To simplify and integrate diverse data sources and analytical tools.
To facilitate the study of ligand binding sites and interactions.

Main Methods:

LigDig is a modular web server comprising seven distinct tools.
It integrates freely available databases (ChEMBL, PubChem, SABIO-RK) and software (cytoscape.js, PDB2PQR, ProBiS, Fconv).
Tools enable free-text compound search, ligand suitability assessment, interaction network analysis, structure comparison, and file preparation.

Main Results:

LigDig provides a streamlined approach to querying and analyzing protein-ligand complex data.
Users can perform complex analyses, such as comparing binding site structures and identifying potential inhibitors.
The server supports batch searches and preparation of files for further computational studies.

Conclusions:

LigDig offers a valuable, user-friendly resource for researchers in bioinformatics and cheminformatics.
It reduces the complexity of analyzing protein-ligand interactions, accelerating research.
The integrated platform enhances the exploration of ligand binding and function.