DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques

A Comprehensive Review of Feature Based Methods for Drug Target Interaction Prediction

(2019) Kanica Sachdev et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Predicting Drug-Target Interaction Network Using Deep Learning Model

(2019) Jiaying You et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Network-based characterization of drug-protein interaction signatures with a space-efficient approach

(2019) Yasuo Tabei et al.   BMC Systems Biology

Revealing Drug-Target Interactions with Computational Models and Algorithms

(2019) Liqian Zhou et al.   MOLECULES

L2,1-GRMF: an improved graph regularized matrix factorization method to predict drug-target interactions

(2019) Zhen Cui et al.   BMC BIOINFORMATICS

Improved Prediction of Drug–Target Interactions Using Self-Paced Learning with Collaborative Matrix Factorization

(2019) Liang-Yong Xia et al.   Journal of Chemical Information and Modeling

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

(2019) Ingoo Lee et al.   PLoS Computational Biology

Gradient Boosting Decision Tree-Based Method for Predicting Interactions Between Target Genes and Drugs

(2019) Ping Xuan et al.   Frontiers in Genetics

Survey of Similarity-based Prediction of Drug-protein Interactions

(2019) Chen Wang et al.   CURRENT MEDICINAL CHEMISTRY

Smote-variants: A python implementation of 85 minority oversampling techniques

(2019) György Kovács   NEUROCOMPUTING

Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities

(2019) Maha Thafar et al.   Frontiers in Chemistry

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

OUP accepted manuscript

(2018)   BIOINFORMATICS

Computational prediction of drug–target interactions using chemogenomic approaches: an empirical survey

(2018) Ali Ezzat et al.   BRIEFINGS IN BIOINFORMATICS

Drug-Target Interactions: Prediction Methods and Applications

(2018) Shanmugam Anusuya et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

A Comprehensive Survey of Graph Embedding: Problems, Techniques and Applications

(2018) HongYun Cai et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Graph embedding techniques, applications, and performance: A survey

(2018) Palash Goyal et al.   KNOWLEDGE-BASED SYSTEMS

An integrative approach to develop computational pipeline for drug-target interaction network analysis

(2018) Ankush Bansal et al.   Scientific Reports

End-to-End Learning From Spectrum Data: A Deep Learning Approach for Wireless Signal Identification in Spectrum Monitoring Applications

(2018) Merima Kulin et al.   IEEE Access

Recent advances in the machine learning-based drug-target interaction prediction

(2018) Wen Zhang et al.   CURRENT DRUG METABOLISM

Integration of k-means clustering algorithm with network analysis for drug-target interactions network prediction

(2018) Sara Aghakhani et al.   International Journal of Data Mining and Bioinformatics

Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization

(2017) Ali Ezzat et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

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

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

(2017) Yunan Luo et al.   Nature Communications

A novel descriptor based on atom-pair properties

(2017) Masataka Kuroda   Journal of Cheminformatics

iDTI-ESBoost: Identification of Drug Target Interaction Using Evolutionary and Structural Features with Boosting

(2017) Farshid Rayhan et al.   Scientific Reports

Predicting drug-target interactions by dual-network integrated logistic matrix factorization

(2017) Ming Hao et al.   Scientific Reports

Predicting drug target interactions using meta-path-based semantic network analysis

(2016) Gang Fu et al.   BMC BIOINFORMATICS

A multiple kernel learning algorithm for drug-target interaction prediction

(2016) André C. A. Nascimento et al.   BMC BIOINFORMATICS

Boosting compound-protein interaction prediction by deep learning

(2016) Kai Tian et al.   METHODS

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

The Comparative Toxicogenomics Database: update 2017

(2016) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

DASPfind: new efficient method to predict drug–target interactions

(2016) Wail Ba-alawi et al.   Journal of Cheminformatics

Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction

(2016) Edgar D. Coelho et al.   PLoS Computational Biology

Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction

(2016) Yong Liu et al.   PLoS Computational Biology

KeBABS: an R package for kernel-based analysis of biological sequences: Fig. 1.

(2015) Johannes Palme et al.   BIOINFORMATICS

Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map: Fig. 1.

(2015) Günter Klambauer et al.   BIOINFORMATICS

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Target prediction utilising negative bioactivity data covering large chemical space

(2015) Lewis H. Mervin et al.   Journal of Cheminformatics

Optimizing drug–target interaction prediction based on random walk on heterogeneous networks

(2015) Abhik Seal et al.   Journal of Cheminformatics

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Similarity-based machine learning methods for predicting drug–target interactions: a brief review

(2013) Hao Ding et al.   BRIEFINGS IN BIOINFORMATICS

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

Drug Target Prediction and Repositioning Using an Integrated Network-Based Approach

(2013) Dorothea Emig et al.   PLoS One

Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity

(2013) Kejian Wang et al.   PLoS Computational Biology

Drug target prediction using adverse event report systems: a pharmacogenomic approach

(2012) M. Takarabe et al.   BIOINFORMATICS

Drug–target interaction prediction by learning from local information and neighbors

(2012) Jian-Ping Mei et al.   BIOINFORMATICS

Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis

(2012) Steven B. Smith et al.   PLoS One

A Systematic Prediction of Multiple Drug-Target Interactions from Chemical, Genomic, and Pharmacological Data

(2012) Hua Yu et al.   PLoS One

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Gaussian interaction profile kernels for predicting drug–target interaction

(2011) Twan van Laarhoven et al.   BIOINFORMATICS

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework

(2010) Y. Yamanishi et al.   BIOINFORMATICS

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

Best Practices for QSAR Model Development, Validation, and Exploitation

(2010) Alexander Tropsha   Molecular Informatics

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

Supervised prediction of drug–target interactions using bipartite local models

(2009) Kevin Bleakley et al.   BIOINFORMATICS

T3DB: a comprehensively annotated database of common toxins and their targets

(2009) Emilia Lim et al.   NUCLEIC ACIDS RESEARCH

Fast Gene Ontology based clustering for microarray experiments

(2009) Kristian Ovaska et al.   BioData Mining

ChemmineR: a compound mining framework for R

(2008) Y. Cao et al.   BIOINFORMATICS

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

(2008) Y. Yamanishi et al.   BIOINFORMATICS

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks

(2008) A. P. Davis et al.   NUCLEIC ACIDS RESEARCH