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

You might also read

Related Articles

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

Sort by
Same author

Cheminformatics Microservice V3: a web portal for chemical structure manipulation and analysis.

Journal of cheminformatics·2025
Same author

Analysis of metabolomics and transcriptomics data to assess interactions in microalgal co-culture of Skeletonema marinoi and Prymnesium parvum.

PloS one·2025
Same author

The evolution of open science in cheminformatics: a journey from closed systems to collaborative innovation.

Journal of cheminformatics·2025
Same author

STOUT V2.0: SMILES to IUPAC name conversion using transformer models.

Journal of cheminformatics·2024
Same author

COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database.

Nucleic acids research·2024
Same author

An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package.

Journal of cheminformatics·2024
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
Same journal

Transformer-accelerated discovery of inhibitors targeting the RpsA<sub>Δ438</sub> deletion in PZA-resistant tuberculosis.

Journal of cheminformatics·2026
Same journal

DICL: a manually curated database of ion channels and ligands as a useful platform for drug discovery targeting ion channels.

Journal of cheminformatics·2026
See all related articles

Related Experiment Video

Updated: May 3, 2026

Controlled Photoredox Ring-Opening Polymerization of O-Carboxyanhydrides Mediated by Ni/Zn Complexes
05:48

Controlled Photoredox Ring-Opening Polymerization of O-Carboxyanhydrides Mediated by Ni/Zn Complexes

Published on: November 21, 2017

7.4K

Efficient ring perception for the Chemistry Development Kit.

John W May1, Christoph Steinbeck

  • 1Cheminformatics and Metabolism, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. johnmay@ebi.ac.uk.

Journal of Cheminformatics
|February 1, 2014
PubMed
Summary
This summary is machine-generated.

Optimized algorithms in the Chemistry Development Kit (CDK) significantly accelerate chemical ring perception. This advancement enables faster processing of larger datasets and improves various cheminformatics applications.

More Related Videos

Diffuse Reflectance Infrared Spectroscopic Identification of Dispersant/Particle Bonding Mechanisms in Functional Inks
10:31

Diffuse Reflectance Infrared Spectroscopic Identification of Dispersant/Particle Bonding Mechanisms in Functional Inks

Published on: May 8, 2015

13.1K
Functionalized Spirocyclic Heterocycle Synthesis and Cytotoxicity Assay
05:17

Functionalized Spirocyclic Heterocycle Synthesis and Cytotoxicity Assay

Published on: February 9, 2021

1.7K

Related Experiment Videos

Last Updated: May 3, 2026

Controlled Photoredox Ring-Opening Polymerization of O-Carboxyanhydrides Mediated by Ni/Zn Complexes
05:48

Controlled Photoredox Ring-Opening Polymerization of O-Carboxyanhydrides Mediated by Ni/Zn Complexes

Published on: November 21, 2017

7.4K
Diffuse Reflectance Infrared Spectroscopic Identification of Dispersant/Particle Bonding Mechanisms in Functional Inks
10:31

Diffuse Reflectance Infrared Spectroscopic Identification of Dispersant/Particle Bonding Mechanisms in Functional Inks

Published on: May 8, 2015

13.1K
Functionalized Spirocyclic Heterocycle Synthesis and Cytotoxicity Assay
05:17

Functionalized Spirocyclic Heterocycle Synthesis and Cytotoxicity Assay

Published on: February 9, 2021

1.7K

Area of Science:

  • Cheminformatics
  • Computational Chemistry
  • Software Development

Background:

  • The Chemistry Development Kit (CDK) is an open-source Java library for chemical information processing.
  • Determining chemical rings is crucial for applications like descriptor calculation, stereochemistry, and atom typing.
  • Previous CDK implementations favored non-unique ring descriptions due to performance limitations of unique ring algorithms.

Purpose of the Study:

  • To implement and optimize efficient algorithms for chemical ring perception within the CDK.
  • To improve the speed and accuracy of ring determination for various cheminformatics tasks.
  • To enable the use of unique ring descriptions in all CDK functionalities.

Main Methods:

  • Development and optimization of novel algorithms for ring perception.
  • Benchmarking algorithm performance on publicly available chemical datasets.
  • Analysis of implementation and optimization strategies for real-world applications.

Main Results:

  • New and existing ring types can be computed significantly faster.
  • Performance improvements of over an order of magnitude were observed in several cases.
  • The computation time for unique rings is now comparable to non-unique methods.

Conclusions:

  • Algorithmic enhancements allow for the processing of larger datasets in practical timeframes.
  • Faster ring perception facilitates the use of more appropriate ring types in procedures like aromaticity determination.
  • Improvements in ring perception benefit multiple areas within the CDK, including stereochemistry and atom typing.