PaccMannRL: De novo generation of hit-like anticancer molecules from transcriptomic data via reinforcement learning.
Jannis Born,Jannis Born,Matteo Manica,Ali Oskooei,Joris Cadow,Greta Markert,Greta Markert,María Rodríguez Martínez +7 more
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In this article, a hybrid VAE was used to generate drugs with high predicted efficacy against cell lines or cancer types, using an anticancer drug sensitivity prediction model as reward function.About:
This article is published in iScience.The article was published on 2021-03-05 and is currently open access. It has received 38 citations till now.read more
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De novo molecular design with deep molecular generative models for PPI inhibitors
Jianmin Wang,Yanyi Chu,Jiashun Mao,Hyeon Nae Jeon,Haiyan Jin,Amir Zeb,Yuil Jang,Kwang-Hwi Cho,Tao Song,Kyoung Tai No +9 more
TL;DR: A protein-protein interaction (PPI) targeted drug-likeness dataset is constructed and a deep molecular generative framework is proposed to generate novel drug- likeness molecules from the features of the seed compounds to improve the de novo design of PPI-targeted compounds.
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Leveraging molecular structure and bioactivity with chemical language models for de novo drug design
Michael Moret,Irene Pachón Angona,Leandro Cotos,Shen Yan,Kenneth Atz,Cyrill Brunner,Martin Baumgartner,Francesca Grisoni,O. Schneider +8 more
TL;DR: In this paper , a collection of virtual molecules was created with a generative chemical language model (CLM) for de novo molecular structure generation by learning from a textual representation of molecules.
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DeepTTA: a transformer-based model for predicting cancer drug response
TL;DR: DeepTTA, a novel end-to-end deep learning model that utilizes transformer for drug representation learning and a multilayer neural network for transcriptomic data prediction of the anti-cancer drug responses, is proposed and discovered that anti- cancer drugs bortezomib and dactinomycin provide a potential therapeutic option with multiple clinical indications.
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Potent antibiotic design via guided search from antibacterial activity evaluations
TL;DR: Liang et al. as mentioned in this paper established a framework, MDAGS (Molecular Design via Attribute-Guided Search), to optimize and generate potent antibiotic molecules, which can generate novel compounds with desirable antibacterial activity without the need for extensive expensive and time-consuming evaluations.
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Perplexity-Based Molecule Ranking and Bias Estimation of Chemical Language Models
TL;DR: In this paper , the authors apply the perplexity metric to determine the degree to which the molecules generated by a chemical language model match the desired design objectives, which allows identifying and ranking the most promising molecular designs based on the probabilities learned by the CLM.
References
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The cancer genome atlas pan-cancer analysis project
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Gastier-Foster,Hollie A. Harper,Carmen Helsel,Kristen M. Leraas,Tara M. Lichtenberg,Cynthia McAllister,Nilsa C. Ramirez,Nilsa C. Ramirez,Samantha Sharpe,Lisa Wise,Erik Zmuda,Stephen J. Chanock,Tanja Davidsen,John A. Demchok,Greg Eley,Ina Felau,Margi Sheth,Heidi J. Sofia,Louis M. Staudt,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jiashan Zhang,Larsson Omberg,Adam Margolin,Benjamin J. Raphael,Fabio Vandin,Hsin-Ta Wu,Mark D.M. Leiserson,Stephen C. Benz,Charles J. Vaske,Houtan Noushmehr,Houtan Noushmehr,Denise M. Wolf,Laura van 't Veer,Dimitris Anastassiou,Tai Hsien Ou Yang,Nuria Lopez-Bigas,Abel Gonzalez-Perez,David Tamborero,Zheng Xia,Wei Li,Dong Yeon Cho,Teresa M. Przytycka,Mark P. Hamilton,Sean E. McGuire,Sven Nelander,Sven Nelander,Patrik Johansson,Rebecka Jörnsten,Rebecka Jörnsten,Teresia Kling +379 more
TL;DR: The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA with a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages.
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DrugBank 5.0: a major update to the DrugBank database for 2018
David S. Wishart,Yannick Djoumbou Feunang,An Chi Guo,Elvis J. Lo,Ana Marcu,Jason R. Grant,Tanvir Sajed,Daniel Johnson,Carin Li,Zinat Sayeeda,Nazanin Assempour,Ithayavani Iynkkaran,Yifeng Liu,Adam Maciejewski,Nicola Gale,Alex Wilson,Lucy Chin,Ryan Cummings,Diana Le,Allison Pon,Craig Knox,Michael Wilson +21 more
TL;DR: This year’s update, DrugBank 5.0, represents the most significant upgrade to the database in more than 10 years and significant improvements have been made to the quantity, quality and consistency of drug indications, drug binding data as well as drug-drug and drug-food interactions.
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Extended-Connectivity Fingerprints
David Rogers,Mathew Hahn +1 more
TL;DR: A description of their implementation has not previously been presented in the literature, and ECFPs can be very rapidly calculated and can represent an essentially infinite number of different molecular features.
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The NCI60 human tumour cell line anticancer drug screen
TL;DR: The development, use and productivity of the NCI60 screen are reviewed, highlighting several outcomes that have contributed to advances in cancer chemotherapy.