ArticleBioinformatics (Oxford, England)2016
Reaction Decoder Tool (RDT): extracting features from chemical reactions.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Mechanism-informed rules tunably balance novelty and feasibility of predicted enzymatic reactions.bioRxiv : the preprint server for biology · 2026Article
- SynRXN: An Open Benchmark and Curated Dataset for Computational Reaction Modeling.Scientific data · 2026Article
- CACLENS: A Multitask Deep Learning System for Enzyme Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery.Nucleic acids research · 2026Article
- NOCTIS: open-source toolkit that turns reaction data into actionable graph networks.Journal of cheminformatics · 2025Article
- Metabolite Identification Data in Drug Discovery, Part 1: Data Generation and Trend Analysis.Molecular pharmaceutics · 2025Article
- Computational tools for nonnatural pathway design: Algorithms, applications, and challenges.Biodesign research · 2025Review
- Graph-sequence enhanced transformer for template-free prediction of natural product biosynthesis.Patterns (New York, N.Y.) · 2025Article
- MEANtools integrates multi-omics data to identify metabolites and predict biosynthetic pathways.PLoS biology · 2025Article
- SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases.Journal of chemical information and modeling · 2025Article
- MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome.Microbiome · 2025Article
- Reactivities ofOrganic process research & development · 2024Article
- Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.Journal of cheminformatics · 2024Article
- Developing BioNavi for Hybrid Retrosynthesis Planning.JACS Au · 2024Article
- REME: an integrated platform for reaction enzyme mining and evaluation.Nucleic acids research · 2024Article
- Learning symmetry-aware atom mapping in chemical reactions through deep graph matching.Journal of cheminformatics · 2024Article
- High-throughput prediction of enzyme promiscuity based on substrate-product pairs.Briefings in bioinformatics · 2024Article
- EnzymeMap: curation, validation and data-driven prediction of enzymatic reactions.Chemical science · 2023Article
- Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.Nature biotechnology · 2023Article
- enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledExtracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. AVAILABILITY AND IMPLEMENTATION: This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder CONTACT: : asad@ebi.ac.uk or s9asad@gmail.com.
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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.