Literature DB >> 29595767

Planning chemical syntheses with deep neural networks and symbolic AI.

Marwin H S Segler1,2, Mike Preuss3, Mark P Waller4.   

Abstract

To plan the syntheses of small organic molecules, chemists use retrosynthesis, a problem-solving technique in which target molecules are recursively transformed into increasingly simpler precursors. Computer-aided retrosynthesis would be a valuable tool but at present it is slow and provides results of unsatisfactory quality. Here we use Monte Carlo tree search and symbolic artificial intelligence (AI) to discover retrosynthetic routes. We combined Monte Carlo tree search with an expansion policy network that guides the search, and a filter network to pre-select the most promising retrosynthetic steps. These deep neural networks were trained on essentially all reactions ever published in organic chemistry. Our system solves for almost twice as many molecules, thirty times faster than the traditional computer-aided search method, which is based on extracted rules and hand-designed heuristics. In a double-blind AB test, chemists on average considered our computer-generated routes to be equivalent to reported literature routes.

Mesh:

Year:  2018        PMID: 29595767     DOI: 10.1038/nature25978

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  34 in total

1.  Mastering the game of Go with deep neural networks and tree search.

Authors:  David Silver; Aja Huang; Chris J Maddison; Arthur Guez; Laurent Sifre; George van den Driessche; Julian Schrittwieser; Ioannis Antonoglou; Veda Panneershelvam; Marc Lanctot; Sander Dieleman; Dominik Grewe; John Nham; Nal Kalchbrenner; Ilya Sutskever; Timothy Lillicrap; Madeleine Leach; Koray Kavukcuoglu; Thore Graepel; Demis Hassabis
Journal:  Nature       Date:  2016-01-28       Impact factor: 49.962

2.  Structure-based classification of chemical reactions without assignment of reaction centers.

Authors:  Qing-You Zhang; João Aires-de-Sousa
Journal:  J Chem Inf Model       Date:  2005 Nov-Dec       Impact factor: 4.956

3.  The ROBIA program for predicting organic reactivity.

Authors:  Ingrid M Socorro; Jonathan M Goodman
Journal:  J Chem Inf Model       Date:  2006 Mar-Apr       Impact factor: 4.956

4.  Learning to predict chemical reactions.

Authors:  Matthew A Kayala; Chloé-Agathe Azencott; Jonathan H Chen; Pierre Baldi
Journal:  J Chem Inf Model       Date:  2011-09-02       Impact factor: 4.956

5.  Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction.

Authors:  Marwin H S Segler; Mark P Waller
Journal:  Chemistry       Date:  2017-02-22       Impact factor: 5.236

6.  Automatized Assessment of Protective Group Reactivity: A Step Toward Big Reaction Data Analysis.

Authors:  Arkadii I Lin; Timur I Madzhidov; Olga Klimchuk; Ramil I Nugmanov; Igor S Antipin; Alexandre Varnek
Journal:  J Chem Inf Model       Date:  2016-11-08       Impact factor: 4.956

7.  Time-split cross-validation as a method for estimating the goodness of prospective prediction.

Authors:  Robert P Sheridan
Journal:  J Chem Inf Model       Date:  2013-04-05       Impact factor: 4.956

8.  Generic strategies for chemical space exploration.

Authors:  Jakob L Andersen; Christoph Flamm; Daniel Merkle; Peter F Stadler
Journal:  Int J Comput Biol Drug Des       Date:  2014-05-28

9.  Structure and reaction based evaluation of synthetic accessibility.

Authors:  Krisztina Boda; Thomas Seidel; Johann Gasteiger
Journal:  J Comput Aided Mol Des       Date:  2007-02-09       Impact factor: 4.179

10.  Prediction of Organic Reaction Outcomes Using Machine Learning.

Authors:  Connor W Coley; Regina Barzilay; Tommi S Jaakkola; William H Green; Klavs F Jensen
Journal:  ACS Cent Sci       Date:  2017-04-18       Impact factor: 14.553

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  152 in total

Review 1.  Generative chemistry: drug discovery with deep learning generative models.

Authors:  Yuemin Bian; Xiang-Qun Xie
Journal:  J Mol Model       Date:  2021-02-04       Impact factor: 1.810

2.  Transforming Computational Drug Discovery with Machine Learning and AI.

Authors:  Justin S Smith; Adrian E Roitberg; Olexandr Isayev
Journal:  ACS Med Chem Lett       Date:  2018-10-08       Impact factor: 4.345

Review 3.  Expanding the medicinal chemistry synthetic toolbox.

Authors:  Jonas Boström; Dean G Brown; Robert J Young; György M Keserü
Journal:  Nat Rev Drug Discov       Date:  2018-08-24       Impact factor: 84.694

Review 4.  Looking beyond the hype: Applied AI and machine learning in translational medicine.

Authors:  Tzen S Toh; Frank Dondelinger; Dennis Wang
Journal:  EBioMedicine       Date:  2019-08-26       Impact factor: 8.143

Review 5.  Applications of machine learning in drug discovery and development.

Authors:  Jessica Vamathevan; Dominic Clark; Paul Czodrowski; Ian Dunham; Edgardo Ferran; George Lee; Bin Li; Anant Madabhushi; Parantu Shah; Michaela Spitzer; Shanrong Zhao
Journal:  Nat Rev Drug Discov       Date:  2019-06       Impact factor: 84.694

Review 6.  Deep learning in single-molecule microscopy: fundamentals, caveats, and recent developments [Invited].

Authors:  Leonhard Möckl; Anish R Roy; W E Moerner
Journal:  Biomed Opt Express       Date:  2020-02-27       Impact factor: 3.732

7.  Artificial Intelligence and Personalized Medicine.

Authors:  Nicholas J Schork
Journal:  Cancer Treat Res       Date:  2019

8.  A unified machine-learning protocol for asymmetric catalysis as a proof of concept demonstration using asymmetric hydrogenation.

Authors:  Sukriti Singh; Monika Pareek; Avtar Changotra; Sayan Banerjee; Bangaru Bhaskararao; P Balamurugan; Raghavan B Sunoj
Journal:  Proc Natl Acad Sci U S A       Date:  2020-01-08       Impact factor: 11.205

9.  DeepScreening: a deep learning-based screening web server for accelerating drug discovery.

Authors:  Zhihong Liu; Jiewen Du; Jiansong Fang; Yulong Yin; Guohuan Xu; Liwei Xie
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

10.  What Does the Machine Learn? Knowledge Representations of Chemical Reactivity.

Authors:  Joshua A Kammeraad; Jack Goetz; Eric A Walker; Ambuj Tewari; Paul M Zimmerman
Journal:  J Chem Inf Model       Date:  2020-03-03       Impact factor: 4.956

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