Atom-to-atom Mapping: A Benchmarking Study of Popular Mapping Algorithms and Consensus Strategies.
Sign Up to like & getrecommendations! Published in 2021 at "Molecular informatics"
DOI: 10.1002/minf.202100138
Abstract: In this paper, we compare the most popular Atom-to-Atom Mapping (AAM) tools: ChemAxon,[1] Indigo,[2] RDTool,[3] NameRXN (NextMove),[4] and RXNMapper[5] which implement different AAM algorithms. An open-source RDTool program was optimized, and its modified version ("new… read more here.
Keywords: mapping; mapping benchmarking; consensus; atom mapping ... See more keywords
Bidirectional Graphormer for Reactivity Understanding: Neural Network Trained to Reaction Atom-to-Atom Mapping Task
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00344
Abstract: This work introduces GraphormerMapper, a new algorithm for reaction atom-to-atom mapping (AAM) based on a transformer neural network adopted for the direct processing of molecular graphs as sets of atoms and bonds, as opposed to… read more here.
Keywords: neural network; network; reaction atom; atom mapping ... See more keywords
Machine Learning Guided Atom Mapping of Metabolic Reactions
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.8b00434
Abstract: Atom mapping of a chemical reaction is a mapping between the atoms in the reactant molecules and the atoms in the product molecules. It encodes the underlying reaction mechanism and, as such, constitutes essential information… read more here.
Keywords: machine learning; learning guided; guided atom; reaction ... See more keywords
Extraction of organic chemistry grammar from unsupervised learning of chemical reactions
Sign Up to like & getrecommendations! Published in 2021 at "Science Advances"
DOI: 10.1126/sciadv.abe4166
Abstract: RXNmapper constructs coherent atom-mapping rules from raw chemical reactions using unsupervised training of neural networks. Humans use different domain languages to represent, explore, and communicate scientific concepts. During the last few hundred years, chemists compiled… read more here.
Keywords: extraction organic; chemistry; chemical; atom mapping ... See more keywords
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Cheminformatics"
DOI: 10.1186/s13321-017-0223-1
Abstract: The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same… read more here.
Keywords: atom; metabolic reactions; mapping algorithms; atom mapping ... See more keywords
MetAMDB: Metabolic Atom Mapping Database
Sign Up to like & getrecommendations! Published in 2022 at "Metabolites"
DOI: 10.3390/metabo12020122
Abstract: MetAMDB is an open-source metabolic atom mapping database, providing atom mappings for around 43,000 metabolic reactions. Each atom mapping can be inspected and downloaded either as an RXN file or as a graphic in SVG… read more here.
Keywords: mapping database; metamdb metabolic; metabolic atom; atom mapping ... See more keywords