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

Molecular Structure and Acidity02:34

Molecular Structure and Acidity

21.6K
An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...
21.6K
Acid Strength and Molecular Structure03:05

Acid Strength and Molecular Structure

33.2K
Binary Acids and Bases
In the absence of any leveling effect, the acid strength of binary compounds of hydrogen with nonmetals (A) increases as the H-A bond strength decreases down a group in the periodic table. For group 17, the order of increasing acidity is HF < HCl < HBr < HI. Likewise, for group 16, the order of increasing acid strength is H2O < H2S < H2Se < H2Te. Across a row in the periodic table, the acid strength of binary hydrogen compounds increases with increasing...
33.2K
Lewis Structures of Molecular Compounds and Polyatomic Ions02:54

Lewis Structures of Molecular Compounds and Polyatomic Ions

46.4K
To draw Lewis structures for complicated molecules and molecular ions, it is helpful to follow a step-by-step procedure as outlined:
46.4K
Structure of Benzene: Molecular Orbital Model01:18

Structure of Benzene: Molecular Orbital Model

12.8K
According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).
12.8K
Molecular Models02:00

Molecular Models

43.9K
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.
43.9K
Virtual Work01:20

Virtual Work

1.4K
The principle of virtual work states that if a body is in static and dynamic equilibrium, then the sum of all the virtual work done by all external forces and couple moments for any given virtual displacement must be zero.
In static equilibrium, a body can experience an imaginary or virtual movement, such as displacement or rotation. The virtual work done by a force is equal to the dot product of force and virtual displacement in the direction of the force. When it comes to virtually rotating a...
1.4K

You might also read

Related Articles

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

Sort by
Same author

Hit-To-Lead Optimization of a Pyridylpiperazine Class Against Malaria: Pharmacokinetic Profile and In Vivo Efficacy of Optimized Compounds.

ChemMedChem·2026
Same author

Discovery of an efficacious 2-ethyl-4-phenylthiazole derivative against acute Chagas disease via multiparametric hit-to-lead optimization and in vivo efficacy.

European journal of medicinal chemistry·2026
Same author

In Silico Studies and Biological Evaluation of Thiosemicarbazones as Cruzain-Targeting Trypanocidal Agents for Chagas Disease.

Pharmaceutics·2026
Same author

Synthesis of a novel brominated vinylic fatty acid with antileishmanial activity that effectively inhibits the <i>Leishmania</i> topoisomerase IB enzyme mediated by halogen bond formation.

Pure and applied chemistry. Chimie pure et appliquee·2025
Same author

Hit-to-Lead Studies of Pyrazinylpiperazines against Visceral Leishmaniasis: Pharmacokinetic Profile and <i>In Vivo</i> Efficacy of Potent Compounds against <i>Leishmania infantum</i>.

ACS pharmacology & translational science·2025
Same author

Phenotypic Screening of H<sub>1</sub>-Antihistamines Identifies Promethazine and Rupatadine as Active Compounds Against <i>Toxocara canis</i> Infective Larvae.

Pharmaceuticals (Basel, Switzerland)·2025

Related Experiment Video

Updated: Feb 12, 2026

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology
10:25

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology

Published on: November 22, 2024

700

Practices in Molecular Docking and Structure-Based Virtual Screening.

Ricardo N Dos Santos1, Leonardo G Ferreira2, Adriano D Andricopulo3

  • 1Departamento de Físico-Química, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil.

Methods in Molecular Biology (Clifton, N.J.)
|March 30, 2018
PubMed
Summary

Structure-based drug design (SBDD) integrates experimental and computational methods for drug discovery. This study details molecular docking and virtual screening protocols for targeting PI3Kδ, a key molecule in hematological diseases.

Keywords:
Autodock vinaDrug discoveryMolecular modelingStructure-based drug designX-ray crystallography

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

1.3K
Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16
06:03

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

Published on: July 15, 2019

8.4K

Related Experiment Videos

Last Updated: Feb 12, 2026

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology
10:25

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology

Published on: November 22, 2024

700
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

1.3K
Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16
06:03

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

Published on: July 15, 2019

8.4K

Area of Science:

  • Biochemistry
  • Computational Biology
  • Pharmacology

Background:

  • Drug discovery has advanced due to progress in molecular and structural biology.
  • Techniques like X-ray crystallography and computational methods, such as molecular docking, are crucial.
  • Structure-based drug design (SBDD) has emerged as a key strategy in pharmaceutical R&D.

Purpose of the Study:

  • To outline molecular docking and structure-based virtual screening (SBVS) protocols.
  • To predict the interaction of small molecules with phosphatidylinositol-bisphosphate-kinase PI3Kδ.
  • To provide a detailed evaluation of these computational methods for targeting PI3Kδ in hematological diseases.

Main Methods:

  • Utilized molecular docking and structure-based virtual screening (SBVS) protocols.
  • Focused on predicting small molecule interactions with the PI3Kδ target.
  • Integrated experimental and computational approaches for drug discovery.

Main Results:

  • Detailed protocols for molecular docking and SBVS were described.
  • The interaction of small molecules with PI3Kδ was predicted.
  • The study provides an evaluation of the efficacy of these methods for drug discovery.

Conclusions:

  • Molecular docking and SBVS are effective computational strategies in SBDD.
  • These methods facilitate the identification and optimization of drug candidates.
  • The described protocols can advance the development of therapeutics for hematological diseases targeting PI3Kδ.