Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ligand Binding Sites02:40

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 Sites02:40

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 Sites01:49

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...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
Protein-protein Interfaces02:04

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

Structural and functional characterization of the newly identified Photorhabdus laumondii tumor necrosis factor-like lectin.

The FEBS journal·2025
Same author

The insight into the biology of five homologous lectins produced by the entomopathogenic bacterium and nematode symbiont Photorhabdus laumondii.

Glycobiology·2025
Same author

Bispecific Thio-Linked Disaccharides as Inhibitors of Pseudomonas Aeruginosa Lectins LecA (PA-IL) and LecB (PA-IIL): Dual-Targeting Strategy.

Chemistry (Weinheim an der Bergstrasse, Germany)·2024
Same author

Elucidating the Complex Oxidation Behavior of Aqueous H<sub>3</sub>PO<sub>3</sub> on Pt Electrodes via <i>In Situ</i> Tender X-ray Absorption Near-Edge Structure Spectroscopy at the P <i>K</i>-Edge.

Journal of the American Chemical Society·2024
Same author

Amphiphilic Sialic Acid Derivatives as Potential Dual-Specific Inhibitors of Influenza Hemagglutinin and Neuraminidase.

International journal of molecular sciences·2023
Same author

Oxidation of Aqueous Phosphorous Acid Electrolyte in Contact with Pt Studied by X-ray Photoemission Spectroscopy.

ACS applied materials & interfaces·2023

Related Experiment Video

Updated: Jul 3, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

TRITON: a graphical tool for ligand-binding protein engineering.

Martin Prokop1, Jan Adam, Zdenek Kríz

  • 1National Centre for Biomolecular Research and Department of Biochemistry, Faculty of Science, Masaryk University, Kotlárská 2, 611 37 Brno, Czech Republic.

Bioinformatics (Oxford, England)
|July 8, 2008
PubMed
Summary

The updated TRITON program offers graphical tools for protein mutant modeling and ligand docking. This software aids in designing novel ligand-binding proteins and investigating protein-ligand interactions.

More Related Videos

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Related Experiment Videos

Last Updated: Jul 3, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Area of Science:

  • Biochemistry and Molecular Modeling
  • Computational Drug Design

Background:

  • The TRITON program facilitates the study of protein-ligand interactions.
  • Previous versions required more complex usage for modeling and docking.

Purpose of the Study:

  • To introduce an enhanced version of the TRITON program with improved graphical user interface.
  • To enable user-friendly protein mutant modeling and ligand docking.
  • To support the design of novel ligand-binding proteins and the study of binding mechanisms.

Main Methods:

  • Utilizes external programs MODELLER for protein mutant modeling.
  • Integrates AutoDock for docking ligands into protein mutants.
  • Provides a graphical user interface for streamlined workflow.

Main Results:

  • TRITON now offers intuitive tools for creating and analyzing protein mutants.
  • Ligand docking into engineered protein pockets is simplified.
  • The software facilitates the exploration of protein-ligand binding dynamics.

Conclusions:

  • The new TRITON version enhances the accessibility of protein-ligand interaction studies.
  • It empowers researchers in designing custom ligand-binding proteins.
  • TRITON serves as a versatile tool for computational protein design and analysis.