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In the scope of drug discovery, the molecular design aims to identify novel compounds from the chemical space where the potential drug-like molecules are estimated to be in the order of 10^60 - 10^100.
Learning long-term dependencies with gradient descent is difficult
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Long short-term memory
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Brian K Shoichet · 2004
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Computer-based de novo design of drug-like molecules
Gisbert Schneider and Uli Fechner · 2005
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On the art of compiling and using’drug-like’chemical fragment spaces
Jörg Degen, Christof Wegscheid-Gerlach, Andrea Zaliani, and Matthias Rarey · 2008
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Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions
Peter Ertl and Ansgar Schuffenhauer · 2009
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Chemical space as a source for new drugs
Jean-Louis Reymond, Ruud Van Deursen, Lorenz C Blum, and Lars Ruddigkeit · 2010
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Extended-connectivity fingerprints
David Rogers and Mathew Hahn · 2010
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Structure-based virtual screening for drug discovery: a problem-centric review
Tiejun Cheng, Qingliang Li, Zhigang Zhou, Yanli Wang, and Stephen H Bryant · 2012
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Recognizing pitfalls in virtual screening: a critical review
Thomas Scior, Andreas Bender, Gary Tresadern, José L Medina-Franco, Karina Martínez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, and Dimitris K Agrafiotis · 2012
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Quantifying the chemical beauty of drugs
G Richard Bickerton, Gaia V Paolini, Jérémy Besnard, Sorel Muresan, and Andrew L Hopkins · 2012
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Generating sequences with recurrent neural networks
Alex Graves · 2013
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Razvan Pascanu, Tomas Mikolov, and Yoshua Bengio · 2013
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Auto-encoding variational bayes
Diederik P Kingma and Max Welling · 2013
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Sequence to sequence learning with neural networks
Ilya Sutskever, Oriol Vinyals, and Quoc V Le · 2014
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Empirical evaluation of gated recurrent neural networks on sequence modeling
Junyoung Chung, Caglar Gulcehre, KyungHyun Cho, and Yoshua Bengio · 2014
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A neural attention model for abstractive sentence summarization
Alexander M. Rush, Sumit Chopra, and Jason Weston · 2015
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Neural machine translation by jointly learning to align and translate
Dzmitry Bahdanau, Kyunghyun Cho, and Yoshua Bengio · 2015
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Neural machine translation by jointly learning to align and translate
Dzmitry Bahdanau, Kyunghyun Cho, and Yoshua Bengio · 2015
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Pointer networks
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Zinc 15–ligand discovery for everyone
Teague Sterling and John J Irwin · 2015
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Pubchem substance and compound databases
Sunghwan Kim, Paul A Thiessen, Evan E Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han, Jane He, Siqian He, Benjamin A Shoemaker, et al · 2016
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Google’s neural machine translation system: Bridging the gap between human and machine translation
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Deep reinforcement learning for de novo drug design
Mariya Popova, Olexandr Isayev, and Alexander Tropsha · 2018
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Molecular generative model based on conditional variational autoencoder for de novo molecular design
Jaechang Lim, Seongok Ryu, Jin Woo Kim, and Woo Youn Kim · 2018
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Multi-objective de novo drug design with conditional graph generative model
Yibo Li, Liangren Zhang, and Zhenming Liu · 2018
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Deep learning enables rapid identification of potent ddr1 kinase inhibitors
Alex Zhavoronkov, Yan A Ivanenkov, Alex Aliper, Mark S Veselov, Vladimir A Aladinskiy, Anastasiya V Aladinskaya, Victor A Terentiev, Daniil A Polykovskiy, Maksim D Kuznetsov, Arip Asadulaev, et al · 2019
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Language models are unsupervised multitask learners
Alec Radford, Jeffrey Wu, Rewon Child, David Luan, Dario Amodei, Ilya Sutskever, et al · 2019
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Incorporating copying mechanism in sequence-to-sequence learning
Jiatao Gu, Zhengdong Lu, Hang Li, and Victor OK Li · 2016
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Hybrid computing using a neural network with dynamic external memory
Alex Graves, Greg Wayne, Malcolm Reynolds, Tim Harley, Ivo Danihelka, Agnieszka Grabska-Barwińska, Sergio Gómez Colmenarejo, Edward Grefenstette, Tiago Ramalho, John Agapiou, et al · 2016
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Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin · 2017
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Chemical space mimicry for drug discovery
William Yuan, Dadi Jiang, Dhanya K Nambiar, Lydia P Liew, Michael P Hay, Joshua Bloomstein, Peter Lu, Brandon Turner, Quynh-Thu Le, Robert Tibshirani, et al · 2017
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Molecular generation with recurrent neural networks (rnns)
Esben Jannik Bjerrum and Richard Threlfall · 2017
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Molecular de-novo design through deep reinforcement learning
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Exploring the gdb-13 chemical space using deep generative models
Josep Arús-Pous, Thomas Blaschke, Silas Ulander, Jean-Louis Reymond, Hongming Chen, and Ola Engkvist · 2019
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Guacamol: benchmarking models for de novo molecular design
Nathan Brown, Marco Fiscato, Marwin HS Segler, and Alain C Vaucher · 2019
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A de novo molecular generation method using latent vector based generative adversarial network
Oleksii Prykhodko, Simon Viet Johansson, Panagiotis-Christos Kotsias, Josep Arús-Pous, Esben Jannik Bjerrum, Ola Engkvist, and Hongming Chen · 2019
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Language models are few-shot learners
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Molecular sets (moses): a benchmarking platform for molecular generation models
Daniil Polykovskiy, Alexander Zhebrak, Benjamin Sanchez-Lengeling, Sergey Golovanov, Oktai Tatanov, Stanislav Belyaev, Rauf Kurbanov, Aleksey Artamonov, Vladimir Aladinskiy, Mark Veselov, et al · 2020
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A deep learning approach to antibiotic discovery
Jonathan M Stokes, Kevin Yang, Kyle Swanson, Wengong Jin, Andres Cubillos-Ruiz, Nina M Donghia, Craig R MacNair, Shawn French, Lindsey A Carfrae, Zohar Bloom-Ackermann, et al · 2020
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Direct steering of de novo molecular generation with descriptor conditional recurrent neural networks
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A 3d generative model for structure-based drug design
Shitong Luo, Jiaqi Guan, Jianzhu Ma, and Jian Peng · 2021
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Modeling real estate dynamics using temporal encoding
Chen Jiang, Jingjing Li, Wenlu Wang, and Wei-Shinn Ku · 2021
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Molecular optimization by capturing chemist’s intuition using deep neural networks
Jiazhen He, Huifang You, Emil Sandström, Eva Nittinger, Esben Jannik Bjerrum, Christian Tyrchan, Werngard Czechtizky, and Ola Engkvist · 2021
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https://en.wikipedia.org/wiki/Drug_discovery
Drug discovery · 2022
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https://www.fda.gov/patients/learn-about-drug-and-device-approvals/drug-development-process
The drug development process · 2022
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http://www.rdkit.org/
Rdkit: Open-source cheminformatics software · 2022
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