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 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...
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...
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...

You might also read

Related Articles

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

Sort by
Same author

AI-assisted vocal emotion analysis in forensic interview with children: an exploratory study.

Frontiers in psychology·2026
Same author

Association of long-term 5α-reductase inhibitor use with survival in men with renal cell carcinoma: a nationwide population-based cohort study.

Frontiers in pharmacology·2026
Same author

Longitudinal Changes in the Serum Pepsinogen I/II Ratio With Progression of Gastric Atrophy.

Journal of clinical laboratory analysis·2026
Same author

MotifLeadDB: A Hierarchical Structural Data Set for Congeneric Ligand Binding Activity Change.

Journal of chemical information and modeling·2026
Same author

Structural basis of the sweat odorant HMHA recognition by the human odorant receptor OR52E8.

Communications biology·2026
Same author

A quantitative methodological framework for traffic accident risk estimation using the Swiss Cheese Model.

International journal of injury control and safety promotion·2026

Related Experiment Video

Updated: May 30, 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

LigDockCSA: protein-ligand docking using conformational space annealing.

Woong-Hee Shin1, Lim Heo, Juyong Lee

  • 1Department of Chemistry, Seoul National University, Seoul, Republic of Korea.

Journal of Computational Chemistry
|August 13, 2011
PubMed
Summary

LigDockCSA, a novel protein-ligand docking method, enhances drug design by combining conformational space annealing (CSA) with an improved scoring function. This approach achieves superior accuracy in predicting native-like binding poses compared to existing methods.

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

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

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

Published on: April 3, 2026

Related Experiment Videos

Last Updated: May 30, 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

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

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

Published on: April 3, 2026

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Protein-ligand docking is crucial for structure-based drug design.
  • Effective docking requires efficient search algorithms and accurate scoring functions.

Purpose of the Study:

  • To develop and evaluate LigDockCSA, a new protein-ligand docking method.
  • To improve the accuracy and performance of docking simulations.

Main Methods:

  • Developed LigDockCSA using conformational space annealing (CSA) for global optimization.
  • Integrated AutoDock energy with piecewise linear potential (PLP) torsion energy for scoring.
  • Refined the energy function by adding a torsional energy term to address limitations.

Main Results:

  • CSA identified lower energy binding poses than AutoDock's Lamarckian genetic algorithm.
  • The refined energy function improved CSA's ability to predict native-like poses.
  • LigDockCSA achieved 84.7% accuracy within 2 Å RMSD on the Astex diverse set, outperforming AutoDock (81.7%) and GOLD (80.5%).
  • Performance increased to 89.4% with the inclusion of conformational entropy.

Conclusions:

  • LigDockCSA demonstrates improved protein-ligand docking performance.
  • The combination of CSA and an enhanced scoring function offers a powerful tool for drug design.
  • Further improvements are possible through incorporating conformational entropy into the scoring model.