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,Victoria M. Tran,Anush Chiappino-Pepe,Ahmed H. Badran,Ian W. Andrews,Ian W. Andrews,Ian W. Andrews,Emma J. Chory,George M. Church,Eric D. Brown,Tommi S. Jaakkola,Regina Barzilay,James J. Collins +21 more
Reads0
Chats0
TLDR
A deep neural network capable of predicting molecules with antibacterial activity is trained and a molecule from the Drug Repurposing Hub-halicin- is discovered that is structurally divergent from conventional antibiotics and displays bactericidal activity against a wide phylogenetic spectrum of pathogens.About:
This article is published in Cell.The article was published on 2020-02-20 and is currently open access. It has received 1002 citations till now.read more
Citations
More filters
Journal ArticleDOI
Pleiotropic actions of phenothiazine drugs are detrimental to Gram-negative bacterial persister cells
TL;DR: In this paper , the effects of phenothiazines on cell metabolism and physiology are highly pleiotropic: at sublethal concentrations, they reduce cellular metabolic, transcriptional, and translational activities; impair cell repair and recovery mechanisms; transiently perturb membrane integrity; and disrupt proton motive force by dissipating the proton concentration gradient across the cell membrane.
Journal ArticleDOI
Efficient antibiotics removal via the synergistic effect of manganese ferrite and MoS2.
Huan Yi,Joan C. Chrisler,Huan Yi,Huan Yi,Raphaël Demias-Morisset,Cui Lai,Cui Lai,Eydhah Almatrafi,Xiuqin Huo,Lei Qin,Yukui Fu,Chengyun Zhou,Chengyun Zhou,Chengyun Zhou,Zeng Zhuotong,Zeng Zhuotong,Zeng Zhuotong,Guangming Zeng,Guangming Zeng,Guangming Zeng +19 more
TL;DR: In this article, a photo-Fenton process over manganese ferrite MnFe2O4 and MoS2 composite was used as the catalyst of photo-fenton process, which showed good performance on tetracycline antibiotics degradation.
Journal ArticleDOI
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge.
TL;DR: In this paper, the authors describe the steps that were taken to construct a novel machine learning model that can predict and generalize well, based on the recently described Directed-Message Passing Neural Networks (D-MPNNs).
Journal ArticleDOI
D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19
Yanqing Yang,Deshan Zhou,Xinben Zhang,Yulong Shi,Jiaxin Han,Liping Zhou,Leyun Wu,Minfei Ma,Jin-tian Li,Shaoliang Peng,Zhijian Xu,Wei Zhou +11 more
TL;DR: D3AI-CoV is a platform for target prediction and virtual screening for the discovery of anti-COVID-19 drugs that can serve as a rapid online tool for predicting potential targets for active compounds and for identifying active molecules against a specific target protein for CO VID-19 treatment.
References
More filters
Journal ArticleDOI
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Journal ArticleDOI
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
TL;DR: A simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s), which should be widely useful, especially in genome analysis of E. coli and other bacteria.
Journal ArticleDOI
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.