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 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.
Vesicular Tubular Clusters01:45

Vesicular Tubular Clusters

After budding out from the ER membrane, some COPII vesicles lose their coat and fuse with one another to form larger vesicles and interconnected tubules called vesicular tubular clusters or VTCs. These clusters constitute a compartment at the ER-Golgi interface known as ERGIC (Endoplasmic Reticulum Golgi Intermediate Compartment). The ERGIC is a mobile membrane-bound cargo transport system that sorts proteins secreted from ER and delivers them to the Golgi.
With the help of motor proteins such...
Drug Discovery: Overview01:26

Drug Discovery: Overview

Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
Automated Microbial Diagnostics01:24

Automated Microbial Diagnostics

Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...
Hybridoma Technology01:31

Hybridoma Technology

Hybridoma technology is used for the large-scale production of monoclonal antibodies. Monoclonal antibodies bind to only a single antigenic determinant or epitope. Such antibodies are used in research, diagnostics, and disease therapy. The hybridoma technology established in 1975 by Georges Köhler and Cesar Milstein was awarded the Nobel Prize in Medicine in 1984 for revolutionizing research and therapy.
Hybridoma Selection
Commonly used fusion techniques — electroporation, polyethylene glycol...
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...

You might also read

Related Articles

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

Sort by
Same author

Foliar application of biostimulants improves nutritional and bioactive quality of walnuts.

Journal of the science of food and agriculture·2024
Same author

Nutritional, chemical, and antioxidant screening of selected varieties of lentils (Lens culinaris spp.) from organic and conventional agriculture.

Journal of the science of food and agriculture·2023
Same author

Bioactive properties of greenhouse-cultivated green beans (Phaseolus vulgaris L.) under biostimulants and water-stress effect.

Journal of the science of food and agriculture·2019
Same author

Fucus vesiculosus extracts as natural antioxidants for improvement of physicochemical properties and shelf life of pork patties formulated with oleogels.

Journal of the science of food and agriculture·2019
Same author

The effect of covering material on the yield, quality and chemical composition of greenhouse-grown tomato fruit.

Journal of the science of food and agriculture·2018
Same author

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2.

Cell death & disease·2017

Related Experiment Video

Updated: Jun 7, 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

MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters.

Rui Mv Abreu1, Hugo Jc Froufe, Maria João Rp Queiroz

  • 1CIMO-ESA, Instituto Politécnico de Bragança, Campus de Sta Apolónia, Apartado 1172, 5301-855 Bragança, Portugal. ruiabreu@ipb.pt.

Journal of Cheminformatics
|October 30, 2010
PubMed
Summary
This summary is machine-generated.

MOLA simplifies virtual screening by enabling parallel processing with AutoDock4 and Vina on non-dedicated computer clusters. This tool enhances drug discovery efficiency for researchers without access to specialized computing resources.

More Related Videos

New Features in Visual Dynamics 3.0
05:00

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

Related Experiment Videos

Last Updated: Jun 7, 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

New Features in Visual Dynamics 3.0
05:00

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

Area of Science:

  • Computational Chemistry
  • Drug Discovery
  • Bioinformatics

Background:

  • Virtual screening of small molecules is crucial for drug discovery but often requires significant computational resources and dedicated clusters.
  • Existing software for virtual screening, such as AutoDock4, typically necessitates access to Linux-based computer clusters.
  • There is a lack of software solutions for performing virtual screening with Vina on computer clusters.

Purpose of the Study:

  • To present MOLA, a user-friendly graphical interface tool designed to automate parallel virtual screening.
  • To enable the use of AutoDock4 and Vina for virtual screening on readily available, non-dedicated computer clusters.
  • To provide an accessible solution for large-scale virtual screening without requiring specialized IT infrastructure.

Main Methods:

  • MOLA automates ligand preparation, parallel job distribution for AutoDock4/Vina, and results analysis.
  • It operates within a custom Live CD GNU/Linux environment, booting from CD and clustering computers via Ethernet without altering existing operating systems.
  • The system supports heterogeneous, multi-platform computers and can record results on external drives.

Main Results:

  • MOLA successfully automates parallel virtual screening using AutoDock4 and Vina.
  • The tool provides ranked lists of ligands based on binding energy and active site proximity.
  • A 10-processor cluster achieved a speed-up of 8.64x with AutoDock4 and 8.60x with Vina, demonstrating significant performance gains.

Conclusions:

  • MOLA is an accessible virtual screening tool for users with limited computational resources and expertise.
  • It allows the utilization of available computers as a cluster without impacting their primary operating systems or requiring hard drive installation.
  • The tool enhances the efficiency of virtual screening, making advanced computational methods more widely available in drug discovery.