Drug–target interaction prediction via chemogenomic space: learning-based methods

SuperPred: update on drug classification and target prediction

(2014) Janette Nickel et al.   NUCLEIC ACIDS RESEARCH

DINIES: drug–target interaction network inference engine based on supervised analysis

(2014) Yoshihiro Yamanishi et al.   NUCLEIC ACIDS RESEARCH

Drug–target interaction prediction through domain-tuned network-based inference

(2013) Salvatore Alaimo et al.   BIOINFORMATICS

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

Scalable prediction of compound-protein interactions using minwise hashing

(2013) Yasuo Tabei et al.   BMC Systems Biology

Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization

(2013) Murat Can Cobanoglu et al.   Journal of Chemical Information and Modeling

Inferring Chemogenomic Features from Drug-Target Interaction Networks

(2013) Yoshihiro Yamanishi   Molecular Informatics

Predicting drug–target interaction networks of human diseases based on multiple feature information

(2013) Weiming Yu et al.   PHARMACOGENOMICS

Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile

(2013) Twan van Laarhoven et al.   PLoS One

A Semi-Supervised Method for Drug-Target Interaction Prediction with Consistency in Networks

(2013) Hailin Chen et al.   PLoS One

Predicting Drug-Target Interactions Using Drug-Drug Interactions

(2013) Shinhyuk Kim et al.   PLoS One

Large-scale prediction of drug–target interactions using protein sequences and drug topological structures

(2012) Dong-Sheng Cao et al.   ANALYTICA CHIMICA ACTA

Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers

(2012) Y. Tabei et al.   BIOINFORMATICS

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

(2012) M. Takarabe et al.   BIOINFORMATICS

Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization

(2012) M. Gonen   BIOINFORMATICS

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

(2012) Jian-Ping Mei et al.   BIOINFORMATICS

Drug–target interaction prediction by random walk on the heterogeneous network

(2012) Xing Chen et al.   Molecular BioSystems

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

Predicting subcellular location of apoptosis proteins with pseudo amino acid composition: approach from amino acid substitution matrix and auto covariance transformation

(2011) Xiaoqing Yu et al.   AMINO ACIDS

Gaussian interaction profile kernels for predicting drug–target interaction

(2011) Twan van Laarhoven et al.   BIOINFORMATICS

Kernel-based data fusion improves the drug–protein interaction prediction

(2011) Yong-Cui Wang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Drug discovery in the age of systems biology: the rise of computational approaches for data integration

(2011) Murat Iskar et al.   CURRENT OPINION IN BIOTECHNOLOGY

Enhancing the Accuracy of Chemogenomic Models with a Three-Dimensional Binding Site Kernel

(2011) Jamel Meslamani et al.   Journal of Chemical Information and Modeling

Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions

(2011) Yoshihiro Yamanishi et al.   Journal of Chemical Information and Modeling

Combining Drug and Gene Similarity Measures for Drug-Target Elucidation

(2011) Liat Perlman et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

From in silico target prediction to multi-target drug design: Current databases, methods and applications

(2011) Alexios Koutsoukas et al.   Journal of Proteomics

STITCH 3: zooming in on protein-chemical interactions

(2011) M. Kuhn et al.   NUCLEIC ACIDS RESEARCH

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

Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces

(2010) Zheng Xia et al.   BMC Systems Biology

Computationally Probing Drug-Protein Interactions Via Support Vector Machine

(2010) Yong-Cui Wang et al.   Letters in Drug Design & Discovery

Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features

(2010) Zhisong He et al.   PLoS One

Supervised prediction of drug–target interactions using bipartite local models

(2009) Kevin Bleakley et al.   BIOINFORMATICS

PubChem as a Source of Polypharmacology

(2009) Bin Chen et al.   Journal of Chemical Information and Modeling

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

SIRENE: supervised inference of regulatory networks

(2008) F. Mordelet et al.   BIOINFORMATICS

Protein-ligand interaction prediction: an improved chemogenomics approach

(2008) Laurent Jacob et al.   BIOINFORMATICS

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

(2008) Y. Yamanishi et al.   BIOINFORMATICS

Gene function prediction using labeled and unlabeled data

(2008) Xing-Ming Zhao et al.   BMC BIOINFORMATICS

Large-scale prediction of drug-target relationships

(2008) Michael Kuhn et al.   FEBS LETTERS