A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

Dozens of coronavirus drugs are in development — what happens next?

(2020) Heidi Ledford   NATURE

Rapid repurposing of drugs for COVID-19

(2020) R. Kiplin Guy et al.   SCIENCE

COVID-19 Research in Brief: 30 May to 5 June, 2020

(2020) Thiago Carvalho   NATURE MEDICINE

Identifying Protein Features Responsible for Improved Drug Repurposing Accuracies Using the CANDO Platform: Implications for Drug Design

(2019) William Mangione et al.   MOLECULES

Mining Heterogeneous Network for Drug Repositioning using Phenotypic Information Extracted from Social Media and Pharmaceutical Databases

(2019) Christopher C. Yang et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

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

(2019) Xiangxiang Zeng et al.   BIOINFORMATICS

Pushing the accuracy limit of shape complementarity for protein-protein docking

(2019) Yumeng Yan et al.   BMC BIOINFORMATICS

Realizing drug repositioning by adapting a recommendation system to handle the process

(2018) Makbule Guclin Ozsoy et al.   BMC BIOINFORMATICS

The Cancer Genome Atlas: Creating Lasting Value beyond Its Data

(2018) Carolyn Hutter et al.   CELL

The rise of deep learning in drug discovery

(2018) Hongming Chen et al.   DRUG DISCOVERY TODAY

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

(2018) Alexandra B. Keenan et al.   Cell Systems

Drug repurposing: progress, challenges and recommendations

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

HMDD v3.0: a database for experimentally supported human microRNA–disease associations

(2018) Zhou Huang et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update – from bulk to single-cell expression data

(2018) Awais Athar et al.   NUCLEIC ACIDS RESEARCH

Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets

(2017) Alexandru Korotcov et al.   MOLECULAR PHARMACEUTICS

Expression Atlas: gene and protein expression across multiple studies and organisms

(2017) Irene Papatheodorou et al.   NUCLEIC ACIDS RESEARCH

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

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

Low Data Drug Discovery with One-Shot Learning

(2017) Han Altae-Tran et al.   ACS Central Science

Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks

(2017) Marwin H. S. Segler et al.   ACS Central Science

A standard database for drug repositioning

(2017) Adam S. Brown et al.   Scientific Data

A probabilistic approach for collective similarity-based drug–drug interaction prediction

(2016) Dhanya Sridhar et al.   BIOINFORMATICS

DrugQuest - a text mining workflow for drug association discovery

(2016) Nikolas Papanikolaou et al.   BMC BIOINFORMATICS

Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data

(2016) Alexander Aliper et al.   MOLECULAR PHARMACEUTICS

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing

(2016) Hansaim Lim et al.   PLoS Computational Biology

A bidirectional drug repositioning approach for Parkinson's disease through network-based inference

(2015) Hindol Rakshit et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

DMAP: a connectivity map database to enable identification of novel drug repositioning candidates

(2015) Hui Huang et al.   BMC BIOINFORMATICS

A survey of current trends in computational drug repositioning

(2015) Jiao Li et al.   BRIEFINGS IN BIOINFORMATICS

The SIDER database of drugs and side effects

(2015) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Large-scale Direct Targeting for Drug Repositioning and Discovery

(2015) Chunli Zheng et al.   Scientific Reports

MicroRNAs and anticancer drugs

(2014) Z. Xing et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

A phenome-guided drug repositioning through a latent variable model

(2014) Halil Bisgin et al.   BMC BIOINFORMATICS

Drug–Disease Association and Drug-Repositioning Predictions in Complex Diseases Using Causal Inference–Probabilistic Matrix Factorization

(2014) Jihong Yang et al.   Journal of Chemical Information and Modeling

Drug repositioning by applying ‘expression profiles’ generated by integrating chemical structure similarity and gene semantic similarity

(2014) Fujian Tan et al.   Molecular BioSystems

The Comparative Toxicogenomics Database's 10th year anniversary: update 2015

(2014) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

Construction of Drug Network Based on Side Effects and Its Application for Drug Repositioning

(2014) Hao Ye et al.   PLoS One

DNorm: disease name normalization with pairwise learning to rank

(2013) R. Leaman et al.   BIOINFORMATICS

Drug repositioning for orphan genetic diseases through Conserved Anticoexpressed Gene Clusters (CAGCs)

(2013) Ivan Molineris et al.   BMC BIOINFORMATICS

Computational drug repositioning through heterogeneous network clustering

(2013) Chao Wu et al.   BMC Systems Biology

Pharmaco-miR: linking microRNAs and drug effects

(2013) J. L. Rukov et al.   BRIEFINGS IN BIOINFORMATICS

The challenges, advantages and future of phenome-wide association studies

(2013) Scott J. Hebbring   IMMUNOLOGY

Drug Repurposing for Gastrointestinal Stromal Tumor

(2013) Z. Y. Pessetto et al.   MOLECULAR CANCER THERAPEUTICS

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

HMDD v2.0: a database for experimentally supported human microRNA and disease associations

(2013) Yang Li et al.   NUCLEIC ACIDS RESEARCH

Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties

(2013) Michael P. Menden et al.   PLoS One

SWEETLEAD: an In Silico Database of Approved Drugs, Regulated Chemicals, and Herbal Isolates for Computer-Aided Drug Discovery

(2013) Paul A. Novick et al.   PLoS One

Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

(2013) Yongcui Wang et al.   PLoS One

A Drug Repositioning Approach Identifies Tricyclic Antidepressants as Inhibitors of Small Cell Lung Cancer and Other Neuroendocrine Tumors

(2013) N. S. Jahchan et al.   Cancer Discovery

Drug Repositioning: A Machine-Learning Approach through Data Integration

(2013) Francesco Napolitano et al.   Journal of Cheminformatics

MicroRNAs: regulators of cancer metastasis and epithelial-mesenchymal transition (EMT)

(2013) Xiang-Ming Ding   Chinese Journal of Cancer

Biomarker-Guided Repurposing of Chemotherapeutic Drugs for Cancer Therapy: A Novel Strategy in Drug Development

(2013) Jan Stenvang et al.   Frontiers in Oncology

e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design

(2012) Emilie Pihan et al.   BIOINFORMATICS

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data

(2012) Clare Pacini et al.   BIOINFORMATICS

SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression

(2012) X. Liu et al.   BIOINFORMATICS

SemMedDB: a PubMed-scale repository of biomedical semantic predications

(2012) H. Kilicoglu et al.   BIOINFORMATICS

Transcriptional data: a new gateway to drug repositioning?

(2012) Francesco Iorio et al.   DRUG DISCOVERY TODAY

Systematic identification of pharmacogenomics information from clinical trials

(2012) Jiao Li et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Biomedical text mining and its applications in cancer research

(2012) Fei Zhu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

INDI: a computational framework for inferring drug interactions and their associated recommendations

(2012) Assaf Gottlieb et al.   Molecular Systems Biology

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

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

(2012) Jordi Barretina et al.   NATURE

Use of genome-wide association studies for drug repositioning

(2012) Philippe Sanseau et al.   NATURE BIOTECHNOLOGY

Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses

(2012) Wei Jiang et al.   Scientific Reports

Assessing Drug Target Association Using Semantic Linked Data

(2012) Bin Chen et al.   PLoS Computational Biology

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

(2011) Adriano Barbosa-Silva et al.   BMC BIOINFORMATICS

Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases

(2011) K. Xu et al.   BRIEFINGS IN BIOINFORMATICS

Mining small-molecule screens to repurpose drugs

(2011) S. J. Swamidass   BRIEFINGS IN BIOINFORMATICS

Exploiting drug-disease relationships for computational drug repositioning

(2011) J. T. Dudley et al.   BRIEFINGS IN BIOINFORMATICS

PhenomeNET: a whole-phenome approach to disease gene discovery

(2011) R. Hoehndorf et al.   NUCLEIC ACIDS RESEARCH

Systematic Drug Repositioning Based on Clinical Side-Effects

(2011) Lun Yang et al.   PLoS One

Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

(2011) M. Sirota et al.   Science Translational Medicine

Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

(2010) Bin Chen et al.   BMC BIOINFORMATICS

Genotator: A disease-agnostic tool for genetic annotation of disease

(2010) Dennis P Wall et al.   BMC Medical Genomics

ChemSpider: An Online Chemical Information Resource

(2010) Harry E. Pence et al.   JOURNAL OF CHEMICAL EDUCATION

Repositioning of an existing drug for the neglected tropical disease Onchocerciasis

(2010) Christian Gloeckner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DCDB: Drug combination database

(2009) Y. Liu et al.   BIOINFORMATICS

Supervised prediction of drug–target interactions using bipartite local models

(2009) Kevin Bleakley et al.   BIOINFORMATICS

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Human Disease-Drug Network Based on Genomic Expression Profiles

(2009) Guanghui Hu et al.   PLoS One

Getting Started in Gene Expression Microarray Analysis

(2009) Donna K. Slonim et al.   PLoS Computational Biology

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

(2009) Sarah L. Kinnings et al.   PLoS Computational Biology

Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts

(2009) Jiao Li et al.   PLoS Computational Biology

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces

(2008) Y. Yamanishi et al.   BIOINFORMATICS

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

(2008) D. Cheng et al.   NUCLEIC ACIDS RESEARCH

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE