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

Anchoring Junctions01:03

Anchoring Junctions

5.5K
Anchoring junctions are multiprotein complexes that help cells connect to other cells and the extracellular matrix. Anchoring junctions are present on the lateral and basal surfaces of cells, providing strong and flexible connections. Focal adhesions are often formed due to cell interactions with the ECM substrata, which initiate signal transduction via kinase cascades and other mechanisms. Together, they provide stability and tissue integrity. There are three types of anchoring junctions:...
5.5K
Drag01:23

Drag

517
Drag is a resistive force opposing an object’s motion through a fluid, resulting from surface pressure and shear forces. It comprises two components: a perpendicular one from pressure and a tangential one from shear stress. Accurate drag calculations use pressure and wall shear stress distributions, often determined through Computational Fluid Dynamics (CFD) or wind tunnel testing. The drag coefficient, a dimensionless measure, depends on factors like shape, Reynolds number, Mach number,...
517
Hepatic Portal System01:21

Hepatic Portal System

7.3K
The hepatic portal system, a critical part of our circulatory framework, transports nutrient-laden, deoxygenated blood from the gastrointestinal tract and spleen to the liver. This ingenious system plays an indispensable role in maintaining our body's metabolic equilibrium.
At its core, the hepatic portal vein is the result of a confluence of the superior and inferior mesenteric veins along with the splenic vein. Each of these veins has a unique role. The superior mesenteric vein is...
7.3K
Drag Force and Terminal Speed01:18

Drag Force and Terminal Speed

3.6K
An interesting force in everyday life is the force of drag on an object when it is moving in a fluid. Like friction, the drag force always opposes the motion of an object. Unlike simple friction, the drag force is proportional to some function of the velocity of the object in that fluid. This functionality is complicated and depends upon the shape of the object, its size, its velocity, and the fluid it is in. For most large objects, such as cyclists, cars, and baseballs, that are not moving too...
3.6K
Lipids as Anchors01:32

Lipids as Anchors

7.8K
In the plasma membrane, the lipids forming the bilayer can also act as an anchor to tether proteins to the membrane. The three main types of lipid anchors found in eukaryotes are – prenyl groups, fatty acyl groups, and glycosylphosphatidylinositol or GPI groups. Prenyl and fatty acyl groups act as anchors on the cytosolic surface of the membrane, whereas GPI anchors proteins on the extracellular side.
The carboxy-terminal of most of the prenylated proteins, such as Ras proteins, contains...
7.8K
Drift Velocity01:19

Drift Velocity

5.9K
The high speed of electrical signals results from the fact that the force between charges acts rapidly at a distance. Thus, when a free charge is forced into a wire, the incoming charge pushes other charges ahead due to the repulsive force between like charges. These moving charges move the charges farther down the line. The density of charge in a system cannot easily be increased, so the signal is passed on rapidly. The resulting electrical shock wave moves through the system at nearly the...
5.9K

You might also read

Related Articles

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

Sort by
Same author

p1/s1, a 3'-nucleotidase/nuclease, allows Leishmania major to circumvent host innate immune response mechanisms.

PLoS pathogens·2026
Same author

Orphan G protein-coupled receptor GPRC5B controls macrophage function by facilitating prostaglandin E receptor 2 signaling.

Nature communications·2025
Same author

Evaluation of serum nitric oxide synthase levels in patients with coronary slow flow based on corrected TIMI frame count.

Archives of medical sciences. Atherosclerotic diseases·2024
Same author

Improvement of binding pose prediction of the MR1 covalent ligands by inclusion of simple pharmacophore constraints and structural waters in the docking process.

3 Biotech·2023
Same author

Docetaxel encapsulation in nanoscale assembly micelles of folate-PEG-docetaxel conjugates for targeted fighting against metastatic breast cancer in vitro and in vivo.

International journal of pharmaceutics·2021
Same author

Corrigendum to "Evaluation of the Correlation between Serum Concentrations of Asymmetric Dimethylarginine and Corrected TIMI Frame Count in Patients with Slow Coronary Flow".

International journal of vascular medicine·2021
Same journal

In-silico combinatorial design and pharmacophore modeling of potent antimalarial 4-anilinoquinolines utilizing QSAR and computed descriptors.

SpringerPlus·2017
Same journal

Erratum to: Implication of Paris Agreement in the context of long-term climate mitigation goals.

SpringerPlus·2017
Same journal

Erratum to: Associations between adherence, depressive symptoms and health-related quality of life in young adults with cystic fibrosis.

SpringerPlus·2017
Same journal

Erratum to: Numerical method to compute acoustic scattering effect of a moving source.

SpringerPlus·2017
Same journal

Identifying appropriate protected areas for endangered fern species under climate change.

SpringerPlus·2017
Same journal

An Algorithm to detect balancing of iterated line sigraph.

SpringerPlus·2017
See all related articles

Related Experiment Video

Updated: Mar 14, 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

1.5K

CrossDocker: a tool for performing cross-docking using Autodock Vina.

Jamal Shamsara1

  • 1Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, 91775-1365 Mashhad, Iran.

Springerplus
|September 22, 2016
PubMed
Summary
This summary is machine-generated.

CrossDocker streamlines protein structure analysis by efficiently identifying optimal holo structures. This computational tool significantly reduces the time for docking, data collection, and analysis, aiding researchers in structural biology.

Keywords:
Autodock VinaCross-dockingVirtual screening

More Related Videos

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.9K
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

1.0K

Related Experiment Videos

Last Updated: Mar 14, 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

1.5K
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.9K
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

1.0K

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Cross-docking is a method for selecting the best holo structures from multiple available protein structures.
  • Accurate protein structure determination is crucial for understanding biological function and drug discovery.

Purpose of the Study:

  • To develop and present CrossDocker, a novel computational tool designed to optimize the cross-docking process.
  • To reduce the time and effort required for analyzing multiple protein structures.

Main Methods:

  • CrossDocker utilizes a Python-based approach for efficient structural analysis.
  • The tool automates parameter setting, input preparation, and data handling for multiple docking experiments.

Main Results:

  • CrossDocker significantly decreases the time for parameter setup, input generation, and data analysis.
  • The software facilitates rapid collection and analysis of data from multiple docking runs.

Conclusions:

  • CrossDocker is a user-friendly, executable binary for Windows, written in Python.
  • The tool is available at http://www.pharm-sbg.com, with example datasets provided for user convenience.