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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence 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:

You might also read

Related Articles

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

Sort by
Same author

The Orphanet Nomenclature and Classification of Rare Diseases for Improved Patient Recognition and Data Interoperability: Qualitative and Quantitative Analysis.

JMIR medical informatics·2026
Same author

Rational design and synthesis of a heterocycle scaffold for DNMT3A inhibition.

Bioorganic chemistry·2026
Same author

Comparing Empirical and Physics-Based Models of Intermolecular Dispersion and Repulsion Energies.

Journal of chemical theory and computation·2026
Same author

Mapping the inhibition landscape of P-glycoprotein via conformational ensemble docking.

Scientific reports·2026
Same author

The covalent docking software landscape: features and applications in drug design.

Briefings in bioinformatics·2025
Same author

Mondo: integrating disease terminology across communities.

Genetics·2025

Related Experiment Video

Updated: Jul 6, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening.

Nicolas Sauton1, David Lagorce, Bruno O Villoutreix

  • 1INSERM, U648, 45 rue des Sts Peres, University Paris Descartes, 75006 Paris, France. nicolas.sauton@laposte.net

BMC Bioinformatics
|April 12, 2008
PubMed
Summary

We developed MS-DOCK, an efficient multiple conformation rigid-body docking tool. It significantly reduces computational screening libraries, enabling faster identification of potential therapeutic compounds.

More Related Videos

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

Related Experiment Videos

Last Updated: Jul 6, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

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

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Structural biology

Background:

  • The rapid growth of protein structures and chemical compounds necessitates efficient virtual screening methods.
  • Flexible structure-based virtual screening is computationally intensive and often intractable for many laboratories.
  • Shape complementarity is crucial for protein-ligand interactions, highlighting the need for shape-based screening tools.

Purpose of the Study:

  • To develop an efficient multiple conformation rigid-body docking approach for structure-based virtual screening.
  • To create a tool that facilitates the selection of compounds fitting well into protein binding sites.
  • To reduce the computational burden of large-scale virtual screening protocols.

Main Methods:

  • Developed the Multiconf-DOCK tool to generate multiple conformers for each input ligand.
  • Utilized a rigid-body docking approach based on the DOCK6 program.
  • Applied an optimized docking protocol to screen conformers against seven different receptor-binding sites.

Main Results:

  • The MS-DOCK approach efficiently generated multi-conformer libraries.
  • Rigid-body docking using MS-DOCK significantly reduced the size of the initial screening library for all tested targets.
  • This reduction facilitates subsequent, more computationally demanding flexible docking procedures.

Conclusions:

  • MS-DOCK provides an effective method for generating multi-conformer libraries.
  • The tool serves as a valuable shape-based filtering step in multi-step virtual screening protocols.
  • MS-DOCK significantly shortens computation times for structure-based drug discovery efforts.