Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Videos

Consensus queries in ligand-based virtual screening experiments.

Francois Berenger^1,2, Oanh Vu³, Jens Meiler³

¹Department of Chemistry, Vanderbilt University, Nashville, TN, USA. berenger@bioreg.kyushu-u.ac.jp.

Journal of Cheminformatics

|November 30, 2017

Summary

This summary is machine-generated.

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

Prediction of pre- and postfusion conformations of class I fusion proteins with AlphaFold2.

PloS one·2026

Same author

Structure-guided compound prioritization strategy for virtual screening identifies putative binders for the nuclear receptor LRH-1.

bioRxiv : the preprint server for biology·2026

Same author

Profiling the CFTR Variant Selectivity and Off-Target Interactions of VX-121.

bioRxiv : the preprint server for biology·2026

Same author

EGFR S442 ectodomain mutation confers cetuximab resistance that can be overcome by ERBB2 blockade with trastuzumab-deruxtecan.

Cancer letters·2026

Same author

Lanthipeptide structure prediction and design with Rosetta.

Methods in enzymology·2026

Same author

VUStruct: A compute pipeline for high throughput and personalized structural biology.

PLoS computational biology·2026

Same journal

Computational design of low-volatility lubricants for space using interpretable machine learning.

Journal of cheminformatics·2026

Same journal

OpenStats: how to combine statistics and research data management (RDM) to leverage efficient scientific data analysis by guided statistics.

Journal of cheminformatics·2026

Same journal

Unified heterogeneity-aware benchmark of drug synergy prediction: a cross-study analysis of traditional machine learning and graph deep learning models.

Journal of cheminformatics·2026

Same journal

Count your bits: fingerprint benchmarking to assess broad chemical space representation.

Journal of cheminformatics·2026

Same journal

Sampling out-of-distribution chemical spaces via Bayesian flow.

Journal of cheminformatics·2026

Same journal

Hold on tight: the kinetic profiling of opioid receptor ligands using the CORAL-MD.

Journal of cheminformatics·2026

See all related articles

Consensus methods in virtual screening improve drug discovery by combining multiple active ligands. Ranking by maximum score is best, but consensus fingerprints offer speed advantages for large chemical spaces.

Area of Science:

Computational chemistry
Drug discovery
Bioinformatics

Background:

Ligand-based virtual screening uses known active molecules to identify new drug candidates.
Using multiple active ligands in screening is more effective than using a single ligand.
Consensus queries combine information from multiple ligands via score merging or descriptor combination.

Purpose of the Study:

To evaluate the performance of various consensus methods in ligand-based virtual screening.
To compare the discriminative power and speed of different consensus strategies.

Main Methods:

Benchmarking of four consensus policies and five consensus sizes.
Investigation of three chemical fingerprints: MACCS 166 bits, ECFP4 2048 bits, and MOLPRINT2D.

Keywords:

Chemical fingerprint Consensus query ECFP4 Ligand-based virtual screening (LBVS)MACCS MOLPRINT2D Potency scaling Several bioactives Similarity search Tanimoto score

Related Experiment Videos

Utilized two datasets comprising 3776 active and ~2 million inactive molecules across 19 protein targets.

Main Results:

The optimal consensus method involves ranking candidate molecules by their maximum similarity score against all known active ligands.
Consensus fingerprints can achieve similar screening performance to consensus scores when the number of active ligands is small.
Consensus fingerprints demonstrate superior performance when computational speed (throughput) is a limiting factor.

Conclusions:

Ranking by maximum score is the most effective consensus strategy for virtual screening.
Consensus fingerprints provide a computationally efficient alternative, especially for large-scale screening.
The choice of consensus method depends on the balance between desired accuracy and available computational resources.