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...
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 Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

You might also read

Related Articles

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

Sort by
Same author

PROTAC-Mediated Targeted Degradation of MDM2 Induces Tumor-Suppressive Signaling in Osteosarcoma Cells.

Cells·2026
Same author

Sinapic Acid-Conjugated Gadolinium Complexes as Anti-Inflammatory Theranostic Agents That Target Transforming Growth Factor β‑Activated Kinase 1 (TAK1).

ACS pharmacology & translational science·2025
Same author

Enhancing binding affinity predictions through efficient sampling with a re-engineered BAR method: a test on GPCR targets.

Chemical science·2025
Same author

Development of MDM2-Targeting PROTAC for Advancing Bone Regeneration.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2025
Same author

Accurate protein-ligand binding free energy estimation using QM/MM on multi-conformers predicted from classical mining minima.

Communications chemistry·2024
Same author

1,2,4-trihydroxybenzene induces non-apoptotic cell death via the structural damage of intracellular organelles.

Toxicology and applied pharmacology·2024

Related Experiment Video

Updated: Jun 19, 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

Quantum mechanical scoring for protein docking.

Art E Cho1, Jae Yoon Chung, Minsup Kim

  • 1Department of Biotechnology and Bioinformatics, Korea University, Jochiwon, Chungnam 339-700, Republic of Korea. artcho@korea.ac.kr

The Journal of Chemical Physics
|October 10, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a new molecular docking protocol using quantum mechanical/molecular mechanical calculations for improved accuracy. The method excels, especially in modeling hydrophobic binding sites with pi-pi interactions.

More Related Videos

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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Related Experiment Videos

Last Updated: Jun 19, 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

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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Molecular docking is crucial for predicting ligand-protein interactions.
  • Current methods, often force field-based, face limitations in accurately modeling complex binding sites.
  • Quantum mechanical/molecular mechanical (QM/MM) approaches offer higher accuracy but are computationally intensive.

Purpose of the Study:

  • To develop and validate a novel molecular docking protocol utilizing QM/MM calculations with QM energy as the scoring function.
  • To assess the performance of the new protocol across diverse binding site characteristics compared to conventional methods.
  • To investigate the protocol's efficacy in modeling specific interactions like pi-pi interactions within hydrophobic binding sites.

Main Methods:

  • Development of a QM/MM-based docking protocol.
  • Implementation of quantum mechanical energy as the scoring function.
  • Testing the protocol on three distinct sets of examples representing varied binding site properties.

Main Results:

  • The QM/MM docking protocol demonstrated performance comparable to or exceeding conventional docking methods across all tested groups.
  • The new method showed superior accuracy in modeling hydrophobic binding sites, particularly those with potential pi-pi interactions.
  • Force field-based methods were less effective than QM scoring in accurately representing these specific interactions.

Conclusions:

  • The developed QM/MM docking protocol offers a significant advancement in molecular docking accuracy.
  • This method is particularly advantageous for studying protein targets with hydrophobic binding pockets and pi-pi interactions.
  • The protocol holds promise for enhancing drug discovery and molecular design efforts.