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...
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:
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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...
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

Early-life proteomic and microbiome features signal obesity risk across 26 years of follow-up.

mSystems·2026
Same author

SpheronizaTor: Spherical Voxelization for Interpretable Protein Microenvironment Modeling.

Computational and structural biotechnology journal·2026
Same author

Multifocal Emphysematous Osteomyelitis of the Spine and Pelvis.

Journal of the Belgian Society of Radiology·2026
Same author

The Future Was Yesterday: Artificial Intelligence in Newborn Medicine.

Neonatology·2026
Same author

A novel simulation tool for low-coverage whole-genome sequencing using multivariate Gaussian mixture models.

BMC bioinformatics·2026
Same author

Structure and Spatial Heterogeneity of Chemosynthesis-Based Deep-Sea Archaeal and Bacterial Communities in Western South Atlantic.

Ecology and evolution·2026
Same journal

Extracellular Vesicles from Mesenchymal Stem Cells Alleviate Spinal Cord Injury via the miR-486-5p/PTEN/PI3K/AKT Pathway.

Current drug targets·2026
Same journal

Improving B-cell Linear Epitope Prediction <i>via</i> Multiple Feature Fusion and an Integrated Machine Learning Algorithm.

Current drug targets·2026
Same journal

Mechanistic Insights into the Inhibition of Plasmodium falciparum DNA Gyrase A by Withanolide Derivatives through Integrated Computational Analysis.

Current drug targets·2026
Same journal

Epitranscriptomics in Breast Cancer: The Unveiled Role of RNA Modifications.

Current drug targets·2026
Same journal

Neuroinflammation in Alzheimer's Disease: New Approaches.

Current drug targets·2026
Same journal

FXYD3: A Key Regulator of Ion Homeostasis and Redox Balance in Cancer Biology.

Current drug targets·2026
See all related articles

Related Experiment Video

Updated: Jun 26, 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

Molecular docking algorithms.

Raquel Dias1, Walter Filgueira de Azevedo

  • 1Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.

Current Drug Targets
|January 9, 2009
PubMed
Summary
This summary is machine-generated.

Virtual screening of small molecule databases aids in discovering novel drug inhibitors. This review details molecular docking algorithms and optimization strategies to enhance simulation accuracy and speed for drug discovery.

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

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach
10:01

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

Related Experiment Videos

Last Updated: Jun 26, 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

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach
10:01

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Molecular modeling

Background:

  • Virtual screening (VS) enables identification of potential inhibitors against biological targets.
  • Molecular docking simulates receptor-ligand complex conformations to predict binding.
  • Various search algorithms are employed by docking programs to predict complex conformations.

Purpose of the Study:

  • To review molecular docking search algorithms and associated software.
  • To discuss optimization methods for virtual screening accuracy and efficiency.

Main Methods:

  • Description of diverse molecular docking search algorithms.
  • Analysis of programs utilizing these search methodologies.
  • Exploration of techniques to enhance virtual screening accuracy.

Main Results:

  • Overview of current molecular docking algorithms.
  • Identification of programs employing specific search strategies.
  • Methods for improving the speed and accuracy of virtual screening simulations.

Conclusions:

  • Molecular docking is a key technique in virtual screening for drug discovery.
  • Understanding and optimizing docking algorithms can accelerate the identification of potential drug candidates.
  • The review provides insights into selecting appropriate algorithms for efficient and accurate virtual screening.