Deep learning for drug repurposing: Methods, databases, and applications

Artificial intelligence framework identifies candidate targets for drug repurposing in Alzheimer’s disease

(2022) Jiansong Fang et al.   Alzheimers Research & Therapy

AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer’s drug discovery

(2021) Yadi Zhou et al.   Alzheimers Research & Therapy

Artificial intelligence, machine learning, and drug repurposing in cancer

(2021) Ziaurrehman Tanoli et al.   Expert Opinion on Drug Discovery

Multimodal single-cell/nucleus RNA sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer's disease

(2021) Jielin Xu et al.   GENOME RESEARCH

Causal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing

(2021) Anastasiya Belyaeva et al.   Nature Communications

Generating functional protein variants with variational autoencoders

(2021) Alex Hawkins-Hooker et al.   PLoS Computational Biology

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications

(2021) Zitao Song et al.   Nature Communications

Cardiac risk stratification in cancer patients: A longitudinal patient–patient network analysis

(2021) Yuan Hou et al.   PLOS MEDICINE

Efficacy and safety of baricitinib for the treatment of hospitalised adults with COVID-19 (COV-BARRIER): a randomised, double-blind, parallel-group, placebo-controlled phase 3 trial

(2021) Vincent C Marconi et al.   Lancet Respiratory Medicine

UDSMProt: universal deep sequence models for protein classification

(2020) Nils Strodthoff et al.   BIOINFORMATICS

Network-based prediction of drug–target interactions using an arbitrary-order proximity embedded deep forest

(2020) Xiangxiang Zeng et al.   BIOINFORMATICS

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Harnessing big ‘omics’ data and AI for drug discovery in hepatocellular carcinoma

(2020) Bin Chen et al.   Nature Reviews Gastroenterology & Hepatology

Machine and deep learning approaches for cancer drug repurposing

(2020) Naiem T. Issa et al.   SEMINARS IN CANCER BIOLOGY

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments

(2020) Lifan Chen et al.   BIOINFORMATICS

Machine learning models for drug–target interactions: current knowledge and future directions

(2020) Sofia D’Souza et al.   DRUG DISCOVERY TODAY

Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker

(2020) Miquel Duran-Frigola et al.   NATURE BIOTECHNOLOGY

Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2

(2020) Yadi Zhou et al.   Cell Discovery

Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing

(2020) Zichen Wang et al.   BIOINFORMATICS

Transfer Learning for Drug Discovery

(2020) Chenjing Cai et al.   JOURNAL OF MEDICINAL CHEMISTRY

Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning

(2020) Xiangxiang Zeng et al.   JOURNAL OF PROTEOME RESEARCH

Dexamethasone in Hospitalized Patients with Covid-19 — Preliminary Report

(2020)   NEW ENGLAND JOURNAL OF MEDICINE

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

(2020) Sepideh Sadegh et al.   Nature Communications

MDeePred: Novel Multi-Channel protein featurization for deep learning based binding affinity prediction in drug discovery

(2020) A S Rifaioglu et al.   BIOINFORMATICS

DeepPurpose: a deep learning library for drug–target interaction prediction

(2020) Kexin Huang et al.   BIOINFORMATICS

SNF–CVAE: Computational method to predict drug–disease interactions using similarity network fusion and collective variational autoencoder

(2020) Tamer N. Jarada et al.   KNOWLEDGE-BASED SYSTEMS

A Comprehensive Survey on Graph Neural Networks

(2020) Zonghan Wu et al.   IEEE Transactions on Neural Networks and Learning Systems

ADMET modeling approaches in drug discovery

(2019) Leonardo L.G. Ferreira et al.   DRUG DISCOVERY TODAY

DeepAffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks

(2019) Mostafa Karimi et al.   BIOINFORMATICS

deepDR: A network-based deep learning approach to in silico drug repositioning

(2019) Xiangxiang Zeng et al.   BIOINFORMATICS

Applications of machine learning in drug discovery and development

(2019) Jessica Vamathevan et al.   NATURE REVIEWS DRUG DISCOVERY

SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules

(2019) Antoine Daina et al.   NUCLEIC ACIDS RESEARCH

MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease

(2019) Jaclyn N. Taroni et al.   Cell Systems

MOLI: multi-omics late integration with deep neural networks for drug response prediction

(2019) Hossein Sharifi-Noghabi et al.   BIOINFORMATICS

Multi-channel PINN: investigating scalable and transferable neural networks for drug discovery

(2019) Munhwan Lee et al.   Journal of Cheminformatics

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

(2019) Ingoo Lee et al.   PLoS Computational Biology

Convolutional Neural Network and Bidirectional Long Short-Term Memory-Based Method for Predicting Drug–Disease Associations

(2019) Xuan et al.   Cells

Predicting Drug–Target Interaction Using a Novel Graph Neural Network with 3D Structure-Embedded Graph Representation

(2019) Jaechang Lim et al.   Journal of Chemical Information and Modeling

Pushing the Boundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism

(2019) Zhaoping Xiong et al.   JOURNAL OF MEDICINAL CHEMISTRY

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

(2019) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

Insights into Computational Drug Repurposing for Neurodegenerative Disease

(2019) Manish D. Paranjpe et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Deep learning for drug–drug interaction extraction from the literature: a review

(2019) Tianlin Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

PathBank: a comprehensive pathway database for model organisms

(2019) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

A genome-wide positioning systems network algorithm for in silico drug repurposing

(2019) Feixiong Cheng et al.   Nature Communications

Deep learning for drug response prediction in cancer

(2019) Delora Baptista et al.   BRIEFINGS IN BIOINFORMATICS

Deep learning-based clustering approaches for bioinformatics

(2019) Md Rezaul Karim et al.   BRIEFINGS IN BIOINFORMATICS

Therapies for rare diseases: therapeutic modalities, progress and challenges ahead

(2019) Erik Tambuyzer et al.   NATURE REVIEWS DRUG DISCOVERY

Rethinking drug design in the artificial intelligence era

(2019) Petra Schneider et al.   NATURE REVIEWS DRUG DISCOVERY

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

(2018) Fangping Wan et al.   BIOINFORMATICS

Compound-protein Interaction Prediction with End-to-end Learning of Neural Networks for Graphs and Sequences

(2018) Masashi Tsubaki et al.   BIOINFORMATICS

Learned protein embeddings for machine learning

(2018) Kevin K Yang et al.   BIOINFORMATICS

Computational drug repositioning for rare diseases in the era of precision medicine

(2018) Brian Delavan et al.   DRUG DISCOVERY TODAY

The rise of deep learning in drug discovery

(2018) Hongming Chen et al.   DRUG DISCOVERY TODAY

Recent Trends in Deep Learning Based Natural Language Processing [Review Article]

(2018) Tom Young et al.   IEEE Computational Intelligence Magazine

Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition

(2018) Sabrina Jaeger et al.   Journal of Chemical Information and Modeling

MoleculeNet: a benchmark for molecular machine learning

(2018) Zhenqin Wu et al.   Chemical Science

Network-based approach to prediction and population-based validation of in silico drug repurposing

(2018) Feixiong Cheng et al.   Nature Communications

OUP accepted manuscript

(2018)   Database-The Journal of Biological Databases and Curation

Cancer Drug Response Profile scan (CDRscan): A Deep Learning Model That Predicts Drug Effectiveness from Cancer Genomic Signature

(2018) Yoosup Chang et al.   Scientific Reports

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

(2018) David Tamborero et al.   Genome Medicine

Planning chemical syntheses with deep neural networks and symbolic AI

(2018) Marwin H. S. Segler et al.   NATURE

The Comparative Toxicogenomics Database: update 2019

(2018) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data

(2018) Fergus Imrie et al.   Journal of Chemical Information and Modeling

Drug repurposing: progress, challenges and recommendations

(2018) Sudeep Pushpakom et al.   NATURE REVIEWS DRUG DISCOVERY

DrugCentral 2018: an update

(2018) Oleg Ursu et al.   NUCLEIC ACIDS RESEARCH

Probes & Drugs portal: an interactive, open data resource for chemical biology

(2017) Ctibor Skuta et al.   NATURE METHODS

Deep Convolutional Neural Networks for Image Classification: A Comprehensive Review

(2017) Waseem Rawat et al.   NEURAL COMPUTATION

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

A machine-learned computational functional genomics-based approach to drug classification

(2016) Jörn Lötsch et al.   EUROPEAN JOURNAL OF CLINICAL PHARMACOLOGY

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

Crowdsourcing biomedical research: leveraging communities as innovation engines

(2016) Julio Saez-Rodriguez et al.   NATURE REVIEWS GENETICS

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Drug Repurposing: New Treatments for Zika Virus Infection?

(2016) Feixiong Cheng et al.   TRENDS IN MOLECULAR MEDICINE

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis

(2016) Feixiong Cheng et al.   PLoS Computational Biology

Active-learning strategies in computer-assisted drug discovery

(2015) Daniel Reker et al.   DRUG DISCOVERY TODAY

Protein localization vector propagation: a method for improving the accuracy of drug repositioning

(2015) Yunku Yeu et al.   Molecular BioSystems

Deep learning

(2015) Yann LeCun et al.   NATURE

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

(2015) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

DGIdb 2.0: mining clinically relevant drug–gene interactions

(2015) Alex H. Wagner et al.   NUCLEIC ACIDS RESEARCH

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

In Silicotarget fishing: addressing a “Big Data” problem by ligand-based similarity rankings with data fusion

(2014) Xian Liu et al.   Journal of Cheminformatics

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Pharmacogenomics Knowledge for Personalized Medicine

(2012) M Whirl-Carrillo et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

SuperTarget goes quantitative: update on drug-target interactions

(2011) N. Hecker et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH