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

Causes of Similarity-Dissimilarity Effect01:26

Causes of Similarity-Dissimilarity Effect

The similarity-dissimilarity effect, a fundamental concept in social psychology, explains how interpersonal similarities and differences influence attraction and social interactions. This effect is supported by three key psychological perspectives: balance theory, social comparison theory, and consensual validation.Balance Theory and Cognitive ConsistencyBalance theory, developed by Fritz Heider, posits that individuals seek cognitive consistency in their relationships. When two people share...
Microtubule Associated Proteins (MAPs)01:42

Microtubule Associated Proteins (MAPs)

Microtubule function and architecture are regulated by an array of specialized proteins called microtubule-associated proteins or MAPs. These proteins are widespread across different organisms and have conserved protein motifs, like the multi-TOG domain for tubulin binding found in the CLASP family of MAPs. Some MAPs are lineage-specific based on their conserved domains. Their functions depend upon the cytoskeletal architecture and cell type they are located within. In-plant cells, a specific...
Wilcoxon Signed-Ranks Test for Matched Pairs01:09

Wilcoxon Signed-Ranks Test for Matched Pairs

The Wilcoxon signed-rank test for matched pairs evaluates the null hypothesis by combining the ranks of differences with their signs. It essentially tests whether the median of the differences in a population of matched pairs is zero. Since the test incorporates more information than the sign test, it generally yields more trustable conclusions. This test also does not require the data to follow a normal distribution, but two conditions must be met for it to be applicable: (1) the data must...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

You might also read

Related Articles

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

Sort by
Same author

In Silico ADMET: From Current Practices to Novel Profilers.

Journal of medicinal chemistry·2026
Same author

Catalytic Asymmetric Hydration of Alkenes.

Journal of the American Chemical Society·2026
Same author

Predicting Enantioselectivity via Kinetic Simulations on Gigantic Reaction Path Networks.

ACS central science·2026
Same author

Current Insights on Skin Permeability Data and Quantitative Structure-Property Relationship Modeling.

Molecular informatics·2026
Same author

Interpretable and Scalable Similarity Metrics for DNA-Encoded Library Design Using Generative Topographic Mapping.

Molecular informatics·2026
Same author

Toward Reaction Vessel Mimicry: Machine Learning-Assisted Automated Exploration of Alkene Polymerization and Its Transferability.

Journal of chemical theory and computation·2026

Related Experiment Video

Updated: May 22, 2026

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps
08:59

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps

Published on: October 28, 2018

Using self-organizing maps to accelerate similarity search.

Fanny Bonachera1, Gilles Marcou, Natalia Kireeva

  • 1Laboratoire d'Infochimie UMR 7177, Université de Strasbourg, 1, rue B. Pascal, 67000 Strasbourg, France.

Bioorganic & Medicinal Chemistry
|May 19, 2012
PubMed
Summary

Self-organizing maps (SOM) accelerate chemical similarity searches using high-dimensional descriptors. Optimal SOMs, built with diverse training sets and gradual training, enhance virtual screening efficiency without sacrificing analogue retrieval.

More Related Videos

Using Informational Connectivity to Measure the Synchronous Emergence of fMRI Multi-voxel Information Across Time
07:12

Using Informational Connectivity to Measure the Synchronous Emergence of fMRI Multi-voxel Information Across Time

Published on: July 1, 2014

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments
08:12

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments

Published on: March 1, 2022

Related Experiment Videos

Last Updated: May 22, 2026

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps
08:59

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps

Published on: October 28, 2018

Using Informational Connectivity to Measure the Synchronous Emergence of fMRI Multi-voxel Information Across Time
07:12

Using Informational Connectivity to Measure the Synchronous Emergence of fMRI Multi-voxel Information Across Time

Published on: July 1, 2014

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments
08:12

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments

Published on: March 1, 2022

Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Machine learning in drug discovery

Background:

  • Self-organizing maps (SOM) are established for chemical space mapping.
  • Classical similarity searches often rely on binary fingerprints, limiting applicability to high-dimensional real-value descriptors.

Purpose of the Study:

  • To leverage SOMs for accelerating similarity searches with high-dimensional descriptors.
  • To define and optimize SOMs for enhanced virtual screening (VS) performance.

Main Methods:

  • Utilized fuzzy tricentric pharmacophore (FPT) and ISIDA substructure counts as descriptors.
  • Positioned compounds on SOMs and searched neighboring neurons for analogues.
  • Developed an enhancement criterion balancing search time and retrieval rates.
  • Investigated training set size and iteration effects on SOM quality.

Main Results:

  • Achieved similarity search acceleration by restricting analogue searches to neighboring SOM neurons.
  • Demonstrated that excessive training set size and iterations can be detrimental.
  • Identified gradual training with en-route checking as an optimal strategy.
  • Successfully accelerated large-scale VS (12,000 queries vs. 160,000 compounds).

Conclusions:

  • SOMs effectively accelerate similarity searches for high-dimensional descriptors.
  • Optimal SOMs can be built from smaller, diverse training sets.
  • Gradual training protocols improve SOM performance for virtual screening enhancement.