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Related Experiment Video

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques.

Hongjian Li1, Kwong-S Leung2, Man-H Wong2

  • 1Institute of Future Cities, Chinese University of Hong Kong, Hong Kong.

Nucleic Acids Research
|April 24, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces USR-VS, a web server for rapid, large-scale virtual screening using Ultrafast Shape Recognition (USR) and its pharmacophoric extension (USRCAT). It identifies potential drug leads by matching 3D molecular shapes and properties, accelerating drug discovery.

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Area of Science:

  • Computational Chemistry
  • Drug Discovery
  • Bioinformatics

Background:

  • Ligand-based virtual screening (VS) identifies molecules with similar activity profiles to a query molecule.
  • 3D similarity methods in VS can uncover novel chemical scaffolds for drug design.
  • Ultrafast Shape Recognition (USR) and its extension USRCAT show promise for discovering molecules with unknown activities.

Purpose of the Study:

  • To present USR-VS, the first web server for large-scale prospective VS using USR and USRCAT.
  • To enable rapid identification of molecules with similar 3D shape and pharmacophoric properties to a query molecule.

Main Methods:

  • Development of the USR-VS web server (http://usr.marseille.inserm.fr/).
  • Screening of 93.9 million 3D conformers from 23.1 million purchasable molecules using USR and USRCAT.
  • Ranking and presentation of the top 100 most similar molecules based on 3D shape and pharmacophoric properties.

Main Results:

  • USR-VS screens millions of molecules in seconds (approx. 2s).
  • Identifies the 100 most similar molecules based on 3D shape and pharmacophoric features.
  • Provides interactive visualization and vendor information for selected hits.

Conclusions:

  • USR-VS facilitates efficient, large-scale prospective virtual screening.
  • The web server supports drug discovery by providing access to novel chemical entities.
  • Enables rapid experimental testing of potential drug leads identified through 3D similarity searches.