Atom‐to‐atom Mapping: A Benchmarking Study of Popular Mapping Algorithms and Consensus Strategies

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 RDTool”) was considered togeth...

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Published inMolecular Informatics Vol. 41; no. 4; pp. e2100138 - n/a
Main Authors Lin, Arkadii, Dyubankova, Natalia, Madzhidov, Timur I., Nugmanov, Ramil I., Verhoeven, Jonas, Gimadiev, Timur R., Afonina, Valentina A., Ibragimova, Zarina, Rakhimbekova, Assima, Sidorov, Pavel, Gedich, Andrei, Suleymanov, Rail, Mukhametgaleev, Ravil, Wegner, Joerg, Ceulemans, Hugo, Varnek, Alexandre
Format Journal Article
LanguageEnglish
Published Germany Wiley 01.04.2022
Wiley Subscription Services, Inc
Wiley-VCH
Subjects
[CHIM.CHEM]Chemical Sciences/Cheminformatics
Algorithms
atom-to-atom mapping
Benchmarking
Benchmarks
Biochemical Phenomena
chemical reactions
Chemical Sciences
Cheminformatics
data cleaning
Databases, Factual
Datasets
Mapping
Mathematical analysis
data cleaning
atom-to-atom mapping
chemical reactions
Online AccessGet full text
ISSN1868-1743
1868-1751
1868-1751
DOI10.1002/minf.202100138

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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 RDTool”) was considered together with several consensus mapping strategies. The Condensed Graph of Reaction approach was used to calculate chemical distances and develop the “AAM fixer” algorithm for an automatized correction of erroneous mapping. The benchmarking calculations were performed on a Golden dataset containing 1851 manually mapped and curated reactions. The best performing RXNMapper program together with the AMM Fixer was applied to map the USPTO database. The Golden dataset, mapped USPTO and optimized RDTool are available in the GitHub repository https://github.com/Laboratoire‐de‐Chemoinformatique.
AbstractList 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 RDTool”) was considered together with several consensus mapping strategies. The Condensed Graph of Reaction approach was used to calculate chemical distances and develop the “AAM fixer” algorithm for an automatized correction of erroneous mapping. The benchmarking calculations were performed on a Golden dataset containing 1851 manually mapped and curated reactions. The best performing RXNMapper program together with the AMM Fixer was applied to map the USPTO database. The Golden dataset, mapped USPTO and optimized RDTool are available in the GitHub repository https://github.com/Laboratoire‐de‐Chemoinformatique.
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 RDTool” ) was considered together with several consensus mapping strategies. The Condensed Graph of Reaction approach was used to calculate chemical distances and develop the “AAM fixer” algorithm for an automatized correction of erroneous mapping. The benchmarking calculations were performed on a Golden dataset containing 1851 manually mapped and curated reactions. The best performing RXNMapper program together with the AMM Fixer was applied to map the USPTO database. The Golden dataset, mapped USPTO and optimized RDTool are available in the GitHub repository https://github.com/Laboratoire‐de‐Chemoinformatique.
In this paper, we compare the most popular Atom-to-Atom Mapping (AAM) tools: ChemAxon, Indigo, RDTool, NameRXN (NextMove), and RXNMapper which implement different AAM algorithms. An open-source RDTool program was optimized, and its modified version ("new RDTool") was considered together with several consensus mapping strategies. The Condensed Graph of Reaction approach was used to calculate chemical distances and develop the "AAM fixer" algorithm for an automatized correction of erroneous mapping. The benchmarking calculations were performed on a Golden dataset containing 1851 manually mapped and curated reactions. The best performing RXNMapper program together with the AMM Fixer was applied to map the USPTO database. The Golden dataset, mapped USPTO and optimized RDTool are available in the GitHub repository https://github.com/Laboratoire-de-Chemoinformatique.
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 RDTool") was considered together with several consensus mapping strategies. The Condensed Graph of Reaction approach was used to calculate chemical distances and develop the "AAM fixer" algorithm for an automatized correction of erroneous mapping. The benchmarking calculations were performed on a Golden dataset containing 1851 manually mapped and curated reactions. The best performing RXNMapper program together with the AMM Fixer was applied to map the USPTO database. The Golden dataset, mapped USPTO and optimized RDTool are available in the GitHub repository https://github.com/Laboratoire-de-Chemoinformatique.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 RDTool") was considered together with several consensus mapping strategies. The Condensed Graph of Reaction approach was used to calculate chemical distances and develop the "AAM fixer" algorithm for an automatized correction of erroneous mapping. The benchmarking calculations were performed on a Golden dataset containing 1851 manually mapped and curated reactions. The best performing RXNMapper program together with the AMM Fixer was applied to map the USPTO database. The Golden dataset, mapped USPTO and optimized RDTool are available in the GitHub repository https://github.com/Laboratoire-de-Chemoinformatique.
Author Timur I. Madzhidov
Hugo Ceulemans
Joerg Wegner
Jonas Verhoeven
Andrei Gedich
Zarina Ibragimova
Arkadii Lin
Ravil Mukhametgaleev
Alexandre Varnek
Timur R. Gimadiev
Pavel Sidorov
Natalia Dyubankova
Assima Rakhimbekova
Valentina A. Afonina
Rail Suleymanov
R. I. Nugmanov
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Keywords data cleaning
atom-to-atom mapping
chemical reactions
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Snippet 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...
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]...
In this paper, we compare the most popular Atom-to-Atom Mapping (AAM) tools: ChemAxon, Indigo, RDTool, NameRXN (NextMove), and RXNMapper which implement...
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...
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SubjectTerms [CHIM.CHEM]Chemical Sciences/Cheminformatics
Algorithms
atom-to-atom mapping
Benchmarking
Benchmarks
Biochemical Phenomena
chemical reactions
Chemical Sciences
Cheminformatics
data cleaning
Databases, Factual
Datasets
Mapping
Mathematical analysis
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Title Atom‐to‐atom Mapping: A Benchmarking Study of Popular Mapping Algorithms and Consensus Strategies
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https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fminf.202100138
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