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 Experiment Videos

TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time.

Ingo Schellhammer1, Matthias Rarey

  • 1Center for Bioinformatics, Research Group for Computational Molecular Design, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.

Journal of Computer-Aided Molecular Design
|February 13, 2007
PubMed
Summary

This study introduces TrixX, a novel structure-based virtual screening tool that avoids sequential searching for faster drug discovery. TrixX analyzes binding site features to efficiently retrieve matching compounds, significantly reducing computational time.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

PegaPlus─Interactive Machine Learning by Human Observation for Efficient Clustering and Analysis of Structure-Activity Data.

Journal of chemical information and modeling·2026
Same author

Enabling Automatic Generation of Protein-Ligand Complex Data Sets with Atomistic Detail.

Journal of chemical information and modeling·2026
Same author

Guiding Similarity Search in Chemical Fragment Spaces with Weighted Fingerprints.

Journal of chemical information and modeling·2026
Same author

ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data.

Journal of chemical information and modeling·2026
Same author

A bottom-up approach to find lead compounds in expansive chemical spaces.

Communications chemistry·2025
Same author

Correction: SAVI Space-combinatorial encoding of the billion-size synthetically accessible virtual inventory.

Scientific data·2025

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • Traditional structure-based virtual screening is a sequential process.
  • This approach can be time-consuming and computationally intensive.

Purpose of the Study:

  • To present a novel structure-based screening paradigm that avoids sequential searching.
  • To introduce the virtual screening tool TrixX, which implements this novel paradigm.
  • To demonstrate TrixX's efficiency and effectiveness in screening experiments.

Main Methods:

  • Implemented a novel screening paradigm in the virtual screening tool TrixX.
  • TrixX analyzes geometric and physicochemical binding site characteristics.
  • Compounds are drawn from a catalog organized by features using relational database technology.

Related Experiment Videos

  • A key element is a selective geometric descriptor encoding functional group information and spatial arrangements.

    • Main Results:

    • TrixX correctly predicted ligand functional group locations in a re-docking experiment with 200 protein-ligand complexes.
    • Retrospective virtual screening experiments on four targets showed enrichment factors comparable to FlexX and FlexX-Scan.
    • Computing times were under one second per compound, nearly two orders of magnitude faster than standard FlexX.

    Conclusions:

    • TrixX offers a significant advancement over traditional virtual screening methods.
    • The tool enables sublinear runtime behavior, drastically improving screening speed.
    • TrixX represents one of the fastest virtual screening tools available for drug discovery.