Conformer-RL: A deep reinforcement learning library for conformer generation
dc.contributor.author | Jiang, Runxuan | |
dc.contributor.author | Gogineni, Tarun | |
dc.contributor.author | Kammeraad, Joshua | |
dc.contributor.author | He, Yifei | |
dc.contributor.author | Tewari, Ambuj | |
dc.contributor.author | Zimmerman, Paul M. | |
dc.date.accessioned | 2022-10-05T15:51:30Z | |
dc.date.available | 2023-11-05 11:51:29 | en |
dc.date.available | 2022-10-05T15:51:30Z | |
dc.date.issued | 2022-10-15 | |
dc.identifier.citation | Jiang, Runxuan; Gogineni, Tarun; Kammeraad, Joshua; He, Yifei; Tewari, Ambuj; Zimmerman, Paul M. (2022). "Conformer-RL: A deep reinforcement learning library for conformer generation." Journal of Computational Chemistry 43(27): 1880-1886. | |
dc.identifier.issn | 0192-8651 | |
dc.identifier.issn | 1096-987X | |
dc.identifier.uri | https://hdl.handle.net/2027.42/174916 | |
dc.description.abstract | 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.Conformer-RL is an open-source Python package for generating conformers of molecules and polymers using deep reinforcement learning. The package includes pretrained models for generating conformers of several classes of covalently bonded molecules as well as a robust library for training and evaluating tailored models for custom molecules and tasks. | |
dc.publisher | John Wiley & Sons, Inc. | |
dc.subject.other | conformer generation | |
dc.subject.other | graph neural network | |
dc.subject.other | machine learning | |
dc.subject.other | reinforcement learning | |
dc.title | Conformer-RL: A deep reinforcement learning library for conformer generation | |
dc.type | Article | |
dc.rights.robots | IndexNoFollow | |
dc.subject.hlbsecondlevel | Chemical Engineering | |
dc.subject.hlbsecondlevel | Chemistry | |
dc.subject.hlbsecondlevel | Materials Science and Engineering | |
dc.subject.hlbtoplevel | Engineering | |
dc.subject.hlbtoplevel | Science | |
dc.description.peerreviewed | Peer Reviewed | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/174916/1/jcc26984.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/174916/2/jcc26984_am.pdf | |
dc.identifier.doi | 10.1002/jcc.26984 | |
dc.identifier.source | Journal of Computational Chemistry | |
dc.identifier.citedreference | M. J. Orella, T. Z. H. Gani, J. V. Vermaas, M. L. Stone, E. M. Anderson, G. T. Beckham, F. R. Brushett, Y. Román-Leshkov, ACS Sustainable Chem. Eng. 2019, 7, 18313. | |
dc.identifier.citedreference | A. L. Dewyer, A. J. Argüelles, P. M. Zimmerman, WIREs Comput Mol Sci 2018, 8, e1354. | |
dc.identifier.citedreference | T. A. Halgren, R. B. Nachbar, J. Comput. Chem. 1996, 17, 587. | |
dc.identifier.citedreference | T. Schulz-Gasch, C. Schärfer, W. Guba, M. Rarey, J. Chem. Inf. Model. 2012, 52, 1499. | |
dc.identifier.citedreference | Y. Wu, E. Mansimov, R. B. Grosse, S. Liao, J. Ba, in Advances in Neural Information Processing Systems, Vol. 30 (Eds: I. Guyon, U. V. Luxburg, S. Bengio, H. Wallach, R. Fergus, S. Vishwanathan, R. Garnett ), Red Hook, NY: Curran Associates, 2017. https://proceedings.neurips.cc/paper/2017/file/361440528766bbaaaa1901845cf4152b-Paper.pdf | |
dc.identifier.citedreference | T. Gogineni, Z. Xu, E. Punzalan, R. Jiang, J. Kammeraad, A. Tewari, P. Zimmerman, in Advances in Neural Information Processing Systems, Vol. 33 (Eds: H. Larochelle, M. Ranzato, R. Hadsell, M. F. Balcan, H. Lin ), Red Hook, NY: Curran Associates, 2020, p. 20142. | |
dc.identifier.citedreference | E. Liang, R. Liaw, R. Nishihara, P. Moritz, R. Fox, K. Goldberg, J. Gonzalez, M. Jordan, I. Stoica, in Proceedings of the 35th International Conference on Machine Learning (Eds: J. Dy, A. Krause ), PMLR, 2018, p. 3053. | |
dc.identifier.citedreference | G. Brockman, V. Cheung, L. Pettersson, J. Schneider, J. Schulman, J. Tang, W. Zaremba, Openai Gym 2016. https://arxiv.org/pdf/1606.01540.pdf | |
dc.identifier.citedreference | A. Paszke, S. Gross, F. Massa, A. Lerer, J. Bradbury, G. Chanan, T. Killeen, Z. Lin, N. Gimelshein, L. Antiga, A. Desmaison, A. Kopf, E. Yang, Z. DeVito, M. Raison, A. Tejani, S. Chilamkurthy, B. Steiner, L. Fang, J. Bai, S. Chintala, in Advances in Neural Information Processing Systems 32 (Eds: H. Wallach, H. Larochelle, A. Beygelzimer, F. D.’. Alché-Buc, E. Fox, R. Garnett ), Red Hook, NY: Curran Associates, 2019, p. 8024 http://papers.neurips.cc/paper/9015-pytorch-an-imperative-style-high-performance-deep-learning-library.pdf | |
dc.identifier.citedreference | G. Landrum, rdkit, 2016. https://github.com/rdkit/rdkit/releases/tag/Release_2016_09_4 | |
dc.identifier.citedreference | N. M. O’Boyle, T. Vandermeersch, C. J. Flynn, A. R. Maguire, G. R. Hutchison, J Cheminform 2011, 3, 1. | |
dc.identifier.citedreference | N. M. O’Boyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch, G. R. Hutchison, Aust. J. Chem. 2011, 3, 33. https://doi.org/10.1186/1758-2946-3-33 | |
dc.identifier.citedreference | L. Turcani, A. Tarzia, F. T. Szczypiński, K. E. Jelfs, J Chem Phys 2021, 154, 214102. | |
dc.identifier.citedreference | L. T. Steven Bennett, A. Tarzia, stko, 2021. https://github.com/JelfsMaterialsGroup/stko | |
dc.identifier.citedreference | X. Wu, S. Wang, J Phys Chem B 1998, 102, 7238. | |
dc.identifier.citedreference | M. Abadi, A. Agarwal, P. Barham, E. Brevdo, Z. Chen, C. Citro, G. S. Corrado, A. Davis, J. Dean, M. Devin, S. Ghemawat, I. Goodfellow, A. Harp, G. Irving, M. Isard, Y. Jia, R. Jozefowicz, L. Kaiser, M. Kudlur, J. Levenberg, D. Mane, R. Monga, S. Moore, D. Murray, C. Olah, M. Schuster, J. Shlens, B. Steiner, I. Sutskever, K. Talwar, P. Tucker, V. Vanhoucke, V. Vasudevan, F. Viegas, O. Vinyals, P. Warden, M. Wattenberg, M. Wicke, Y. Yu, X. Zheng, TensorFlow (Version v2.8.2), 2015. https://static.googleusercontent.com/media/research.google.com/en//pubs/archive/45166.pdf | |
dc.identifier.citedreference | C. Cai, S. Wang, Y. Xu, W. Zhang, K. Tang, Q. Ouyang, L. Lai, J. Pei, J. Med. Chem. 2020, 63, 8683. | |
dc.identifier.citedreference | S. Narvekar, J. Sinapov, M. Leonetti, P. Stone, Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2016), Singapore, 2016. | |
dc.identifier.citedreference | M. Fey, J. E. Lenssen, ICLR Workshop on Representation Learning on Graphs and Manifolds, New Orleans, USA, 2019. | |
dc.identifier.citedreference | J. Schulman, F. Wolski, P. Dhariwal, A. Radford, O. Klimov, Proximal Policy Optim Algorith 2017, 1707, 06347. | |
dc.identifier.citedreference | D. Silver, T. Hubert, J. Schrittwieser, I. Antonoglou, M. Lai, A. Guez, M. Lanctot, L. Sifre, D. Kumaran, T. Graepel, T. Lillicrap, K. Simonyan, D. Hassabis, Science 2018, 362, 1140. | |
dc.identifier.citedreference | O. Vinyals, I. Babuschkin, W. M. Czarnecki, M. Mathieu, A. Dudzik, J. Chung, D. H. Choi, R. Powell, T. Ewalds, P. Georgiev, J. Oh, D. Horgan, M. Kroiss, I. Danihelka, A. Huang, L. Sifre, T. Cai, J. P. Agapiou, M. Jaderberg, A. S. Vezhnevets, R. Leblond, T. Pohlen, V. Dalibard, D. Budden, Y. Sulsky, J. Molloy, T. L. Paine, C. Gulcehre, Z. Wang, T. Pfaff, Y. Wu, R. Ring, D. Yogatama, D. Wünsch, K. McKinney, O. Smith, T. Schaul, T. Lillicrap, K. Kavukcuoglu, D. Hassabis, C. Apps, D. Silver, Nature 2019, 575, 350. | |
dc.identifier.citedreference | Y. Li, H. Kang, K. Ye, S. Yin, X. Li, Conference on Neural Information Processing Systems Deep Reinforcement Learning Workshop, Montréal, Canada, 2018. https://arxiv.org/abs/1812.00967 | |
dc.identifier.citedreference | Z. Zhou, X. Li, R. N. Zare, ACS Cent. Sci. 2017, 3, 1337. | |
dc.identifier.citedreference | G. Simm, R. Pinsler, J. M. Hernandez-Lobato, in Proceedings of the 37th International Conference on Machine Learning, Vol. 119 (Eds: H. D. III, A. Singh ), PMLR, 2020, p. 8959 http://proceedings.mlr.press/v119/simm20b.html | |
dc.identifier.citedreference | J.-P. Ebejer, G. M. Morris, C. M. Deane, J. Chem. Inf. Model. 2012, 52, 1146. | |
dc.identifier.citedreference | J. C. Cole, O. Korb, P. McCabe, M. G. Read, R. Taylor, J. Chem. Inf. Model. 2018, 58, 615. | |
dc.working.doi | NO | en |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.