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

Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

66.1K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
66.1K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

20.5K
20.5K
Ligand Binding Sites02:40

Ligand Binding Sites

15.8K
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...
15.8K
Ligand Binding Sites02:40

Ligand Binding Sites

9.1K
9.1K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

6.0K
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...
6.0K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.3K
4.3K

You might also read

Related Articles

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

Sort by
Same author

The SLC15A4-LAMTOR1 interaction licenses endolysosomal TLR-mediated mTOR signaling and inflammatory cytokine production.

bioRxiv : the preprint server for biology·2026
Same author

Author Correction: Posttranslational modifications remodel proteome-wide ligandability.

Nature chemical biology·2026
Same author

Genetic and pharmacological inactivation of peptidoglycan remodeling increases antibiotic susceptibility of vancomycin-resistant Enterococcus faecium.

Nature communications·2026
Same author

Posttranslational modifications remodel proteome-wide ligandability.

Nature chemical biology·2026
Same author

Inspiring discovery through reviews and visualization in biochemistry.

Trends in biochemical sciences·2026
Same author

Genetic and pharmacological inactivation of peptidoglycan remodeling increases antibiotic susceptibility of vancomycin-resistant <i>Enterococcus faecium</i>.

bioRxiv : the preprint server for biology·2026
Same journal

Computational design of blue melanin by motif-scaffolding a pentapeptide-repeat protein.

Protein science : a publication of the Protein Society·2026
Same journal

Mechanism-guided mutagenesis of Rft1 to test its role as a dolichol-linked oligosaccharide scramblase in cells.

Protein science : a publication of the Protein Society·2026
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
See all related articles

Related Experiment Video

Updated: Apr 8, 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

1.6K

Covalent docking using autodock: Two-point attractor and flexible side chain methods.

Giulia Bianco1, Stefano Forli2, David S Goodsell2

  • 1Department of Life and Environmental Sciences, Drug Sciences Section, University of Cagliari, via Ospedale 72, Cagliari, 09124, Italy.

Protein Science : a Publication of the Protein Society
|June 25, 2015
PubMed
Summary
This summary is machine-generated.

We present two automated covalent docking methods in Autodock4. The flexible side chain method accurately predicted ligand poses in 75% of protein-ligand complexes, offering a reliable computational tool.

Keywords:
computational dockingcomputer-aided drug designcovalent inhibitorsligand-protein interactions

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

1.3K
Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

11.9K

Related Experiment Videos

Last Updated: Apr 8, 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

1.6K
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

1.3K
Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

11.9K

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Automated covalent docking is crucial for predicting drug-target interactions.
  • Accurate pose prediction is essential for understanding binding mechanisms and designing new therapeutics.

Purpose of the Study:

  • To evaluate two novel automated covalent docking methods within Autodock4.
  • To assess the reliability of these methods in predicting crystallographic poses of ligands in covalent complexes.

Main Methods:

  • Implementation and application of the two-point attractor method for covalent docking.
  • Implementation and application of the flexible side chain method for covalent docking.
  • Validation using a training set of 20 diverse protein-ligand covalent complexes.

Main Results:

  • The flexible side chain method achieved successful pose prediction in 75% of tested covalent complexes.
  • The two-point attractor method also demonstrated utility, though with lower success rates.
  • Performance was notably impacted by inhibitor size, with larger molecules posing greater challenges.

Conclusions:

  • The flexible side chain method represents a significant advancement in automated covalent docking accuracy.
  • These freely available tools can aid researchers in structure-based drug design and lead optimization.
  • Further refinement may be needed to address challenges with larger or more complex inhibitors.