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

Autocrine Signaling01:01

Autocrine Signaling

48.1K
Autocrine signaling is one of the many signaling mechanisms that function inside multicellular organisms to carry out intercellular communication. In this type of signaling mechanism, the same cell that secretes an extracellular signaling molecule also expresses the receptors to bind and respond to that signaling molecule.
Autocrine Signaling in Macrophages
Under normal physiological conditions, autocrine signaling is essential for maintaining homeostasis. This process is well characterized in...
48.1K
The Vestibular System01:29

The Vestibular System

39.6K
The vestibular system is a set of inner ear structures that provide a sense of balance and spatial orientation. This system is comprised of structures within the labyrinth of the inner ear, including the cochlea and two otolith organs—the utricle and saccule. The labyrinth also contains three semicircular canals—superior, posterior, and horizontal—that are oriented on different planes.
39.6K
Pinocytosis00:43

Pinocytosis

65.7K
Cells use energy-requiring bulk transport mechanisms to transfer large particles, or large amounts of small particles, into or out of the cell. The cells envelop the particles in spherical membranes called vesicles or vacuoles. Vesicles that transport material into the cell are built from the cell membrane. These vesicles encapsulate external molecules and transport them into the cell in a process called endocytosis.
65.7K
Synaptic Signaling01:12

Synaptic Signaling

75.1K
Neurons communicate at synapses, or junctions, to excite or inhibit the activity of other neurons or target cells, such as muscles. Synapses may be chemical or electrical.
75.1K

You might also read

Related Articles

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

Sort by
Same author

Genetic Variants in the Transcription Factor Network: The Impact of <i>FOXC1, NOTCH1, RORC, FOXC</i>2 and <i>SOX18</i> in Primary Lymphedema.

Lymphology·2025
Same author

Genetic Variants in <i>LZTR1, MAP2K1</i> and <i>RAF1</i>: Insights into the Role of RAS-MAPK Pathway in Primary Lymphedema.

Lymphology·2025
Same author

A cross-correlator-based timing tool for FemtoMAX.

Journal of synchrotron radiation·2025
Same author

Genetic Study of HGF-MET Signaling Pathway in Primary Lymphedema Patients: Supporting Evidence for Loss of Function Variants in HGF.

Lymphology·2025
Same author

Genetic Variants in Genes Correlated to the PI3K/AKT Pathway: The Role of <i>ARAP3, CDH5, KIF11</i> and <i>RELN</i> in Primary Lymphedema.

Lymphology·2024
Same author

An Updated Classification of Primary Lymphedema Based on Age of Onset, Lymphatic Anomalies, and Genetics.

Lymphology·2024

Related Experiment Video

Updated: Jul 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

175

MAGI-Dock: a PyMOL companion to Autodock Vina.

J Kaftalli1, A Bernini, G Bonetti

  • 1MAGI EUREGIO, Bolzano, Italy. jurgen.kaftalli@assomagi.org.

European Review for Medical and Pharmacological Sciences
|December 19, 2023
PubMed
Summary

MAGI-Dock simplifies molecular docking by integrating Autodock Vina and PyMOL into a user-friendly graphical interface. This tool lowers the learning curve for molecular docking simulations in both academic and enterprise settings.

More Related Videos

Author Spotlight: Advancing Therapeutics to Treat Vibriosis in Humans and Aquatic Organisms
03:29

Author Spotlight: Advancing Therapeutics to Treat Vibriosis in Humans and Aquatic Organisms

Published on: May 31, 2024

488
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.3K

Related Experiment Videos

Last Updated: Jul 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

175
Author Spotlight: Advancing Therapeutics to Treat Vibriosis in Humans and Aquatic Organisms
03:29

Author Spotlight: Advancing Therapeutics to Treat Vibriosis in Humans and Aquatic Organisms

Published on: May 31, 2024

488
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.3K

Area of Science:

  • Structural Biology
  • Medicinal Chemistry
  • Computational Drug Discovery

Background:

  • Molecular docking simulations are crucial for drug discovery and structural biology research.
  • Current free docking software, like Autodock Vina, is command-line based, posing usability challenges.
  • Defining the docking box requires external molecular graphics programs and specialized training, limiting accessibility.

Purpose of the Study:

  • To develop a graphical user interface (GUI) that integrates Autodock Vina and PyMOL.
  • To simplify the process of defining docking parameters, specifically the docking box.
  • To enhance the accessibility and adoption of molecular docking simulations.

Main Methods:

  • Developed MAGI-Dock, a free, open-source graphical user interface.
  • Integrated the functionalities of Autodock Vina and PyMOL.
  • Created a synergistic tool that merges molecular graphics and docking capabilities.

Main Results:

  • MAGI-Dock provides a unified interface for molecular docking and visualization.
  • The GUI simplifies the definition of the docking box, overcoming limitations of command-line tools.
  • The software streamlines the molecular modeling workflow.

Conclusions:

  • MAGI-Dock lowers the learning curve for molecular docking simulations.
  • The tool benefits trainees in academic and enterprise environments.
  • MAGI-Dock enhances the usability of free molecular docking software.