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Development of a Novel Fingerprint for Chemical Reactions and Its Application to Large-Scale Reaction Classification and Similarity

https://doi.org/10.1021/ci5006614
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/9783527618279.ch12openalex-snapshot
Reaction Classification and Knowledge Acquisition
inferredcites →https://doi.org/10.1002/9783527618279.ch43bopenalex-snapshot
Analysis of Reaction Information
inferredcites →https://doi.org/10.1002/cmdc.200700312openalex-snapshot
SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites
inferredcites →https://doi.org/10.1002/minf.201400052openalex-snapshot
A Short Review of Chemical Reaction Database Systems, Computer‐Aided Synthesis Design, Reaction Prediction and Synthetic Feasibility
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Automatic reaction mapping and reaction center detection
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The protein data bank: A computer-based archival file for macromolecular structures
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Classification of organic reactions using similarity
inferredcites →https://doi.org/10.1016/s1574-1400(09)00513-1openalex-snapshot
Annual Reports in Computational Chemistry
inferredcites →https://doi.org/10.1021/ci00046a002openalex-snapshot
Atom pairs as molecular features in structure-activity studies: definition and applications
inferredcites →https://doi.org/10.1021/ci00054a008openalex-snapshot
Topological torsion: a new molecular descriptor for SAR applications. Comparison with other descriptors
inferredcites →https://doi.org/10.1021/ci00057a005openalex-snapshot
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
inferredcites →https://doi.org/10.1021/ci00068a008openalex-snapshot
CASREACT: more than a million reactions
inferredcites →https://doi.org/10.1021/ci00068a023openalex-snapshot
Building and refining a knowledge base for synthetic organic chemistry via the methodology of inductive and deductive machine learning
inferredcites →https://doi.org/10.1021/ci0503208openalex-snapshot
Molecular Transformations as a Way of Finding and Exploiting Consistent Local QSAR
inferredcites →https://doi.org/10.1021/ci100050topenalex-snapshot
Extended-Connectivity Fingerprints
inferredcites →https://doi.org/10.1021/ci300116popenalex-snapshot
Mining Electronic Laboratory Notebooks: Analysis, Retrosynthesis, and Reaction Based Enumeration
inferredcites →https://doi.org/10.1021/ci400442fopenalex-snapshot
Algorithm for Reaction Classification
inferredcites →https://doi.org/10.1021/ci800413mopenalex-snapshot
Knowledge-Based Approach to de Novo Design Using Reaction Vectors
inferredcites →https://doi.org/10.1021/ci9803381openalex-snapshot
Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets
inferredcites →https://doi.org/10.1021/jm200187yopenalex-snapshot
The Medicinal Chemist’s Toolbox: An Analysis of Reactions Used in the Pursuit of Drug Candidates
inferredcites →https://doi.org/10.1023/a:1010933404324openalex-snapshot
Random Forests
inferredcites →https://doi.org/10.1039/b602413kopenalex-snapshot
Analysis of the reactions used for the preparation of drug candidate molecules
inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot
ChEMBL: a large-scale bioactivity database for drug discovery
inferredcites →https://doi.org/10.1159/isbn.978-3-8055-9573-5openalex-snapshot
Theilheimer's Synthetic Methods of Organic Chemistry
inferredcites →https://doi.org/10.2307/1932409openalex-snapshot
Measures of the Amount of Ecologic Association Between Species
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python

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Extraction of organic chemistry grammar from unsupervised learning of chemical reactions
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Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome
inferred← citeshttps://doi.org/10.1145/3109859.3109895openalex-snapshot
Chemical Reactant Recommendation Using a Network of Organic Chemistry
inferred← citeshttps://doi.org/10.1145/3746252.3761323openalex-snapshot
Proto-Yield: An Uncertainty-Aware Prototype Network for Yield Prediction in Real-world Chemical Reactions
inferred← citeshttps://doi.org/10.1186/s12859-018-2248-5openalex-snapshot
SimCAL: a flexible tool to compute biochemical reaction similarity
inferred← citeshttps://doi.org/10.1186/s13321-020-00452-5openalex-snapshot
CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration
inferred← citeshttps://doi.org/10.1186/s13321-020-00460-5openalex-snapshot
Molecular representations in AI-driven drug discovery: a review and practical guide
inferred← citeshttps://doi.org/10.1186/s13321-021-00579-zopenalex-snapshot
Uncertainty-aware prediction of chemical reaction yields with graph neural networks
inferred← citeshttps://doi.org/10.1186/s13321-022-00594-8openalex-snapshot
Improving the performance of models for one-step retrosynthesis through re-ranking
inferred← citeshttps://doi.org/10.1186/s13321-023-00715-xopenalex-snapshot
MetaRF: attention-based random forest for reaction yield prediction with a few trails
inferred← citeshttps://doi.org/10.1186/s13321-024-00805-4openalex-snapshot
Enhancing chemical synthesis: a two-stage deep neural network for predicting feasible reaction conditions
inferred← citeshttps://doi.org/10.1186/s13321-024-00815-2openalex-snapshot
Prediction of chemical reaction yields with large-scale multi-view pre-training
inferred← citeshttps://doi.org/10.1186/s13321-024-00834-zopenalex-snapshot
Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices
inferred← citeshttps://doi.org/10.1186/s13321-024-00875-4openalex-snapshot
Reaction rebalancing: a novel approach to curating reaction databases
inferred← citeshttps://doi.org/10.1186/s13321-025-00987-5openalex-snapshot
Enhancing chemical reaction search through contrastive representation learning and human-in-the-loop
inferred← citeshttps://doi.org/10.1186/s13321-025-01118-wopenalex-snapshot
NOCTIS: open-source toolkit that turns reaction data into actionable graph networks
inferred← citeshttps://doi.org/10.1186/s13321-025-01130-0openalex-snapshot
The consolidation of open-source computer-assisted chemical synthesis data into a comprehensive database
inferred← citeshttps://doi.org/10.1360/ssc-2025-0111openalex-snapshot
The converging moment of chemistry and artificial intelligence: a review and outlook
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006471openalex-snapshot
Quantum chemistry reveals thermodynamic principles of redox biochemistry
inferred← citeshttps://doi.org/10.1515/revce-2024-0027openalex-snapshot
Machine learning applications for thermochemical and kinetic property prediction
inferred← citeshttps://doi.org/10.17122/ogbus-2019-4-243-268openalex-snapshot
USING METHOD OF MACHINE TRAINING AND ARTIFICIAL INTELLIGENCE IN CHEMICAL TECHNOLOGY. PART I
inferred← citeshttps://doi.org/10.17586/2226-1494-2020-20-6-863-870openalex-snapshot
Prediction of reaction conditions by deep learning techniques
inferred← citeshttps://doi.org/10.21203/rs.3.rs-10847205/v1openalex-snapshot
Reaction-Center-Guided Reranking of Transformer Product Predictions with a Product-Conditioned Graph Neural Network
inferred← citeshttps://doi.org/10.21203/rs.3.rs-4276245/v1openalex-snapshot
Artificial intelligence-based parametrization of Michaelis–Menten maximal velocity: Toward in silico New Approach Methodologies (NAMs)
inferred← citeshttps://doi.org/10.21203/rs.3.rs-8855497/v1openalex-snapshot
Fragment Tree Reconciliation (FTR) for Space Applications
inferred← citeshttps://doi.org/10.21741/9781644902530-4openalex-snapshot
Artificial Intelligence in Material Genomics
inferred← citeshttps://doi.org/10.26434/chemrxiv-2021-x5sj7openalex-snapshot
National Institutes of Health (NIH) Workshop on Reaction Informatics
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-4kzp1openalex-snapshot
Data-driven Reaction Template Fingerprints
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-nll2jopenalex-snapshot
Bayesian optimisation for additive screening and yieldimprovements in chemical reactions – beyond one-hot encodings
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-nll2j-v2openalex-snapshot
Bayesian optimisation for additive screening and yieldimprovements in chemical reactions – beyond one-hot encoding
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-6rbfjopenalex-snapshot
Recommending Multiple Reaction Conditions UsingTwo-Stage Deep Neural Networks
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-89v4qopenalex-snapshot
Transform Descriptors for template free reaction classification
inferred← citeshttps://doi.org/10.26434/chemrxiv.11659563.v1openalex-snapshot
Integrating Deep Neural Networks and Symbolic Inference for Organic Reactivity Prediction
inferred← citeshttps://doi.org/10.26434/chemrxiv.11869692.v4openalex-snapshot
RetroXpert: Decompose Retrosynthesis Prediction Like A Chemist
inferred← citeshttps://doi.org/10.26434/chemrxiv.13273310openalex-snapshot
Completion of Partial Reaction Equations
inferred← citeshttps://doi.org/10.26434/chemrxiv.13273310.v1openalex-snapshot
Completion of Partial Reaction Equations
inferred← citeshttps://doi.org/10.26434/chemrxiv.13280495openalex-snapshot
A Quick Policy to Filter Reactions Based on Feasibility in AI-Guided Retrosynthetic Planning
inferred← citeshttps://doi.org/10.26434/chemrxiv.13280495.v1openalex-snapshot
A Quick Policy to Filter Reactions Based on Feasibility in AI-Guided Retrosynthetic Planning
inferred← citeshttps://doi.org/10.26434/chemrxiv.8168354.v1openalex-snapshot
Automatic Retrosynthetic Pathway Planning Using Template-free Models
inferred← citeshttps://doi.org/10.26434/chemrxiv.8427776openalex-snapshot
Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks
inferred← citeshttps://doi.org/10.26434/chemrxiv.9897365.v1openalex-snapshot
Data-Driven Chemical Reaction Classification with Attention-Based Neural Networks
inferred← citeshttps://doi.org/10.26434/chemrxiv.9897365.v2openalex-snapshot
Data-Driven Chemical Reaction Classification, Fingerprinting and Clustering using Attention-Based Neural Networks
inferred← citeshttps://doi.org/10.33774/chemrxiv-2021-mc870openalex-snapshot
Reaction Classification and Yield Prediction using the Differential Reaction Fingerprint DRFP
inferred← citeshttps://doi.org/10.3389/fceng.2020.00005openalex-snapshot
Artificial Intelligence for Computer-Aided Synthesis In Flow: Analysis and Selection of Reaction Components
inferred← citeshttps://doi.org/10.3389/fchem.2018.00199openalex-snapshot
Computational Chemical Synthesis Analysis and Pathway Design
inferred← citeshttps://doi.org/10.3390/app13095311openalex-snapshot
Learning Hierarchical Representations for Explainable Chemical Reaction Prediction
inferred← citeshttps://doi.org/10.3390/biom10111486openalex-snapshot
Virtual Screening for Reactive Natural Products and Their Probable Artifacts of Solvolysis and Oxidation
inferred← citeshttps://doi.org/10.48550/arxiv.2012.11522openalex-snapshot
Barking up the right tree: an approach to search over molecule synthesis DAGs
inferred← citeshttps://doi.org/10.48550/arxiv.2104.03279openalex-snapshot
Modern Hopfield Networks for Few- and Zero-Shot Reaction Template Prediction
inferred← citeshttps://doi.org/10.59717/j.xinn-inform.2026.100026openalex-snapshot
A comprehensive survey of AI-based retrosynthesis planning: Datasets, models, and tools
inferred← citeshttps://doi.org/10.6084/m9.figshare.19367575openalex-snapshot
Additional file 1 of Improving the performance of models for one-step retrosynthesis through re-ranking
inferred← citeshttps://doi.org/10.6084/m9.figshare.25059473openalex-snapshot
Additional file 1 of Enhancing chemical synthesis: a two-stage deep neural network for predicting feasible reaction conditions
inferred← citeshttps://doi.org/10.6084/m9.figshare.26685387openalex-snapshot
Additional file 1 of Prediction of chemical reaction yields with large-scale multi-view pre-training
inferred← citeshttps://doi.org/10.6084/m9.figshare.26699678openalex-snapshot
Additional file 1 of Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices
inferred← citeshttps://doi.org/10.6084/m9.figshare.26699681openalex-snapshot
Additional file 2 of Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices
inferred← citeshttps://doi.org/10.70675/ab76b9fcze4cbz45a3z950dz023b6506d0acopenalex-snapshot
Predictive models for kinetic and thermodynamic parameters of reactions
inferred← citeshttps://doi.org/10.7554/elife.82401openalex-snapshot
SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations
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