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Related Concept Videos

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...
Patch Clamp01:18

Patch Clamp

Many fundamental cell functions such as muscle contraction and nerve transmission rely on the electrical signals produced by the movement of positively and negatively charged ions across the cell membrane. One competent method to record current flowing across the whole cell or single ion channel is the patch-clamp technique.
In this method, a glass micropipette containing electrolyte solution is tightly sealed against a small portion of the cell membrane. As a result, a patch of the cell...

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Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface
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VSpipe-GUI, an Interactive Graphical User Interface for Virtual Screening and Hit Selection.

Rashid Hussain1, Andrew Scott Hackett1, Sandra Álvarez-Carretero2

  • 1School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK.

International Journal of Molecular Sciences
|February 24, 2024
PubMed
Summary
This summary is machine-generated.

VSpipe-GUI is a user-friendly, cross-platform tool for computer-aided drug development. It enhances virtual screening with a new spatial filtering module for efficient ligand selection, accelerating drug discovery.

Keywords:
AutoDockAutoDock VinaVSpipeVSpipe-GUIchemoinformaticsdockingdrug designvirtual screening

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • Virtual screening is crucial for computer-aided drug development but often requires specialized users or is platform-limited.
  • Existing tools lack user-friendliness and broad operating system compatibility.
  • Previous work introduced VSpipe, a command-line pipeline for structure-based virtual screening.

Purpose of the Study:

  • To develop an interactive, user-friendly, and cross-platform graphical user interface (GUI) for virtual screening.
  • To enhance the efficiency and accessibility of virtual screening processes.
  • To introduce a novel compound selection module for targeted ligand identification.

Main Methods:

  • Developed VSpipe-GUI, a Python-based toolkit with an interactive GUI.
  • Implemented a new spatial filtering module for compound selection based on binding site features.
  • Tested VSpipe-GUI using AutoDock Vina for docking against the Hepatitis C Virus NS3 protease.

Main Results:

  • VSpipe-GUI offers improved user-friendliness and accessibility across multiple operating systems (Linux, Windows, Mac OS X).
  • The new implementation demonstrates significantly faster docking performance compared to the previous version.
  • The spatial filtering module efficiently and specifically selected ligands interacting with the target binding site (HCV NS3 catalytic serine 139).

Conclusions:

  • VSpipe-GUI democratizes virtual screening by providing an accessible and efficient tool for drug discovery.
  • The spatial filtering module represents a significant advancement in identifying relevant compounds from large chemical libraries.
  • This enhanced pipeline accelerates the identification of potential drug candidates for therapeutic targets.