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Conformer‐RL: A deep reinforcement learning library for conformer generation

Conformer‐RL is an open‐source Python package for applying deep reinforcement learning (RL) to the task of generating a diverse set of low‐energy conformations for a single molecule. The library features a simple interface to train a deep RL conformer generation model on any covalently bonded molecu...

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Detalles Bibliográficos
Autores principales: Jiang, Runxuan, Gogineni, Tarun, Kammeraad, Joshua, He, Yifei, Tewari, Ambuj, Zimmerman, Paul M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9542157/
https://www.ncbi.nlm.nih.gov/pubmed/36000759
http://dx.doi.org/10.1002/jcc.26984
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author Jiang, Runxuan
Gogineni, Tarun
Kammeraad, Joshua
He, Yifei
Tewari, Ambuj
Zimmerman, Paul M.
author_facet Jiang, Runxuan
Gogineni, Tarun
Kammeraad, Joshua
He, Yifei
Tewari, Ambuj
Zimmerman, Paul M.
author_sort Jiang, Runxuan
collection PubMed
description Conformer‐RL is an open‐source Python package for applying deep reinforcement learning (RL) to the task of generating a diverse set of low‐energy conformations for a single molecule. The library features a simple interface to train a deep RL conformer generation model on any covalently bonded molecule or polymer, including most drug‐like molecules. Under the hood, it implements state‐of‐the‐art RL algorithms and graph neural network architectures tuned specifically for molecular structures. Conformer‐RL is also a platform for researching new algorithms and neural network architectures for conformer generation, as the library contains modular class interfaces for RL environments and agents, allowing users to easily swap components with their own implementations. Additionally, it comes with tools to visualize and save generated conformers for further analysis. Conformer‐RL is well‐tested and thoroughly documented with tutorials for each of the functionalities mentioned above, and is available on PyPi and Github: https://github.com/ZimmermanGroup/conformer-rl.
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spelling pubmed-95421572022-10-14 Conformer‐RL: A deep reinforcement learning library for conformer generation Jiang, Runxuan Gogineni, Tarun Kammeraad, Joshua He, Yifei Tewari, Ambuj Zimmerman, Paul M. J Comput Chem Software Notes Conformer‐RL is an open‐source Python package for applying deep reinforcement learning (RL) to the task of generating a diverse set of low‐energy conformations for a single molecule. The library features a simple interface to train a deep RL conformer generation model on any covalently bonded molecule or polymer, including most drug‐like molecules. Under the hood, it implements state‐of‐the‐art RL algorithms and graph neural network architectures tuned specifically for molecular structures. Conformer‐RL is also a platform for researching new algorithms and neural network architectures for conformer generation, as the library contains modular class interfaces for RL environments and agents, allowing users to easily swap components with their own implementations. Additionally, it comes with tools to visualize and save generated conformers for further analysis. Conformer‐RL is well‐tested and thoroughly documented with tutorials for each of the functionalities mentioned above, and is available on PyPi and Github: https://github.com/ZimmermanGroup/conformer-rl. John Wiley & Sons, Inc. 2022-08-24 2022-10-15 /pmc/articles/PMC9542157/ /pubmed/36000759 http://dx.doi.org/10.1002/jcc.26984 Text en © 2022 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Notes
Jiang, Runxuan
Gogineni, Tarun
Kammeraad, Joshua
He, Yifei
Tewari, Ambuj
Zimmerman, Paul M.
Conformer‐RL: A deep reinforcement learning library for conformer generation
title Conformer‐RL: A deep reinforcement learning library for conformer generation
title_full Conformer‐RL: A deep reinforcement learning library for conformer generation
title_fullStr Conformer‐RL: A deep reinforcement learning library for conformer generation
title_full_unstemmed Conformer‐RL: A deep reinforcement learning library for conformer generation
title_short Conformer‐RL: A deep reinforcement learning library for conformer generation
title_sort conformer‐rl: a deep reinforcement learning library for conformer generation
topic Software Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9542157/
https://www.ncbi.nlm.nih.gov/pubmed/36000759
http://dx.doi.org/10.1002/jcc.26984
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