ArticleJournal of cheminformatics2017
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
Article in Journal of cheminformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 209 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
209 citing papers in PubMed.
- Climate Shapes Elevational Gradients in Concentration, Composition, and Functional Diversity of Willow Metabolomes.Plant, cell & environment · 2026Article
- FastRet: Fast and Simple Retention Time Prediction in Liquid Chromatography.Journal of chemical information and modeling · 2026Article
- Interactive Software for Interpreting and Curating High-Resolution Electron Ionization Mass Spectra.Journal of mass spectrometry : JMS · 2026Article
- Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms.Chemical reviews · 2026Review
- Count your bits: fingerprint benchmarking to assess broad chemical space representation.Journal of cheminformatics · 2026Article
- Machine Learning Approaches for Compound-Target Interaction Prediction: A Review.Foods (Basel, Switzerland) · 2026Review
- Antibacterial Activity and Cytotoxicity Evaluation of 5-Amino-4-cyano-1,3-oxazole Derivatives: Synthesis, In Silico, and In Vitro Studies.Chemistry & biodiversity · 2026Article
- Impact of Chemical Quality on High-Throughput in Vitro Assays: A Tox21 Study.Chemical research in toxicology · 2026Article
- AntibioticDB: An Updated and Improved Open-Access Database for the Antibacterial Research and Development Community.ACS infectious diseases · 2026Article
- FAME3R: an efficient, practical and reliable open-source tool for predicting phase 1 and phase 2 sites of metabolism.Journal of cheminformatics · 2026Article
- SPARFlow: a KNIME workflow for integrated structure-activity or structure-property relationship analysis.Journal of cheminformatics · 2026Article
- MassBank: an open and FAIR mass spectral data resource.Nucleic acids research · 2026Article
- Machine Learning in Homogeneous Catalysis: Basic Concepts and Best Practices.ACS catalysis · 2026Article
- SLICE (SMARTS and Logic In ChEmistry): fast generation of molecules using advanced chemical synthesis logic and modern coding style.Journal of cheminformatics · 2025Article
- Two-Stage Probability-Enhanced Regression on Property Matrices and LLM Embeddings Enables State-of-the-Art Prediction of Gene Knockdown by Modified siRNAs.International journal of molecular sciences · 2025Article
- In Silico Analysis of CMolecules (Basel, Switzerland) · 2025Article
- Active Stacking-Deep Learning with Strategic Sampling for Small and Imbalanced Chemical Toxicity Prediction.ACS omega · 2025Article
- Artificial intelligence modelling of tyrosine kinase inhibitors at risk of malabsorption and bioavailability-enhancing strategies.British journal of clinical pharmacology · 2025Article
- Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders.Briefings in bioinformatics · 2025Article
- Prediction of UGT-mediated phase II metabolism via ligand- and structure-based predictive models.Journal of cheminformatics · 2025Article
149 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms.
resultsWe report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism.
conclusionsThis paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software. Graphical abstract CDK 2.0 provides new features and improved performance.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.