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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TLDR
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 and generative models
TL;DR: In this paper, the authors present de novo approaches according to the coarseness of their molecular representation: that is, whether molecular design is modeled on an atom-based, fragment-based or reaction-based paradigm.
Journal ArticleDOI
TITAN: T-cell receptor specificity prediction with bimodal attention networks
TL;DR: Mann et al. as mentioned in this paper proposed a bimodal neural network that explicitly encodes both TCR sequences and epitopes to enable the independent study of generalization capabilities to unseen TCRs and/or epitopes.
Journal ArticleDOI
De Novo Structure-Based Drug Design Using Deep Learning.
Sowmya Ramaswamy Krishnan,Navneet Bung,Sarveswara Rao Vangala,Rajgopal Srinivasan,Gopalakrishnan Bulusu,Arijit Roy +5 more
TL;DR: This work proposes a deep learning-based method, where the knowledge of the active site structure of the target protein is sufficient to design new molecules, and validated it against two well-studied proteins.
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OUP accepted manuscript
TL;DR: DeepTTA as discussed by the authors is 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.
Journal ArticleDOI
Generative machine learning for de novo drug discovery: A systematic review
TL;DR: A systematic literature review of experimental articles and reviews over the last five years, machine learning models, challenges associated with computational molecule design along with proposed solutions, and molecular encoding methods are discussed in this article .
References
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Generative Model for Proposing Drug Candidates Satisfying Anticancer Properties Using a Conditional Variational Autoencoder.
TL;DR: A conditional variational autoencoder (CVAE) is proposed as a generative model to propose drug candidates with the desired property outside a data set range to solve the problem of syntactically invalid molecules in molecular generative models.
Journal ArticleDOI
Structural similarity assessment for drug sensitivity prediction in cancer
TL;DR: It is shown that it is possible to extend the usefulness of existing screens to untested drugs by deriving substitute sensitivity profiles from structurally similar drugs part of the screen.
Journal Article
Nitro-oxidative Stress Is Involved in Anticancer Activity of 17β-Estradiol Derivative in Neuroblastoma Cells.
TL;DR: It is proposed that 2-methoxyestradiol may be a natural modulator of cancer cell death and survival through nitric oxide generation and reduction of mitochondrial membrane potential through nitro-oxidative stress-dependent mechanisms.
Patent
Lipid-containing compositions and methods of using them
TL;DR: Anabolic compositions can be administered to patients with chronic diseases, or who suffer from conditions precipitated by such diseases or long term treatment regimes, such as organ or tissue transplant procedures as discussed by the authors.
Journal ArticleDOI
Author Correction: DNA damage in circulating leukocytes measured with the comet assay may predict the risk of death.
Stefano Bonassi,Marcello Ceppi,Peter Møller,Amaya Azqueta,Mirta Milić,Monica Neri,Gunnar Brunborg,Roger W. L. Godschalk,Gudrun Koppen,Sabine A. S. Langie,João Paulo Teixeira,João Paulo Teixeira,Marco Bruzzone,Juliana da Silva,Danieli Benedetti,Delia Cavallo,Cinzia Lucia Ursini,Lisa Giovannelli,Silvia Moretti,Patrizia Riso,Cristian Del Bo,Patrizia Russo,Małgorzata M. Dobrzyńska,Irina A. Goroshinskaya,Ekaterina I. Surikova,Marta Staruchova,Magdalena Barancokova,Katarina Volkovova,Alena Kažimı́rová,Bozena Smolkova,Blanca Laffon,Vanessa Valdiglesias,Susana Pastor,Ricard Marcos,Ricard Marcos,Alba Hernández,Alba Hernández,Goran Gajski,Biljana Spremo-Potparević,Lada Živković,Elisa Boutet-Robinet,Hervé Perdry,Pierre Lebailly,Carlos L. Perez,Nurşen Başaran,Zsuzsanna Németh,Anna Safar,Maria Dusinska,Andrew Collins +48 more