4.5 Review

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

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

SuperPred: update on drug classification and target prediction

Janette Nickel et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

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

Yoshihiro Yamanishi et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemical Research Methods

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

Jian-Ping Mei et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

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

Salvatore Alaimo et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Predicting drug-target interactions using restricted Boltzmann machines

Yuhao Wang et al.

BIOINFORMATICS (2013)

Article Mathematical & Computational Biology

Scalable prediction of compound-protein interactions using minwise hashing

Yasuo Tabei et al.

BMC SYSTEMS BIOLOGY (2013)

Article Chemistry, Medicinal

Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization

Murat Can Cobanoglu et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)

Review Chemistry, Medicinal

Inferring Chemogenomic Features from Drug-Target Interaction Networks

Yoshihiro Yamanishi

MOLECULAR INFORMATICS (2013)

Article Multidisciplinary Sciences

Predicting Drug-Target Interactions Using Drug-Drug Interactions

Shinhyuk Kim et al.

PLOS ONE (2013)

Article Biochemical Research Methods

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

Masataka Takarabe et al.

BIOINFORMATICS (2012)

Review Biochemical Research Methods

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

Murat Iskar et al.

CURRENT OPINION IN BIOTECHNOLOGY (2012)

Article Biochemistry & Molecular Biology

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

Xing Chen et al.

MOLECULAR BIOSYSTEMS (2012)

Article Biochemistry & Molecular Biology

STITCH 3: zooming in on protein-chemical interactions

Michael Kuhn et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

ChEMBL: a large-scale bioactivity database for drug discovery

Anna Gaulton et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemical Research Methods

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

Feixiong Cheng et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Gaussian interaction profile kernels for predicting drug-target interaction

Twan van Laarhoven et al.

BIOINFORMATICS (2011)

Article Biology

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

Yong-Cui Wang et al.

COMPUTATIONAL BIOLOGY AND CHEMISTRY (2011)

Article Chemistry, Medicinal

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

Jamel Meslamani et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Medicinal

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

Yoshihiro Yamanishi et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Biochemical Research Methods

Combining Drug and Gene Similarity Measures for Drug-Target Elucidation

Liat Perlman et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2011)

Review Biochemical Research Methods

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

Alexios Koutsoukas et al.

JOURNAL OF PROTEOMICS (2011)

Article Biochemical Research Methods

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

Yoshihiro Yamanishi et al.

BIOINFORMATICS (2010)

Article Mathematical & Computational Biology

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

Zheng Xia et al.

BMC SYSTEMS BIOLOGY (2010)

Article Chemistry, Medicinal

Computationally Probing Drug-Protein Interactions Via Support Vector Machine

Yong-Cui Wang et al.

LETTERS IN DRUG DESIGN & DISCOVERY (2010)

Article Biochemical Research Methods

Supervised prediction of drug-target interactions using bipartite local models

Kevin Bleakley et al.

BIOINFORMATICS (2009)

Article Chemistry, Medicinal

PubChem as a Source of Polypharmacology

Bin Chen et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)

Article Chemistry, Multidisciplinary

AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

Garrett M. Morris et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Multidisciplinary Sciences

Predicting new molecular targets for known drugs

Michael J. Keiser et al.

NATURE (2009)

Article Biochemistry & Molecular Biology

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

Yanli Wang et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemical Research Methods

SIRENE: supervised inference of regulatory networks

Fantine Mordelet et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

Protein-ligand interaction prediction: an improved chemogenomics approach

Laurent Jacob et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

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

Yoshihiro Yamanishi et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

Gene function prediction using labeled and unlabeled data

Xing-Ming Zhao et al.

BMC BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

Large-scale prediction of drug-target relationships

Michael Kuhn et al.

FEBS LETTERS (2008)

Article Biotechnology & Applied Microbiology

Drug-target network

Muhammed A. Yildirim et al.

NATURE BIOTECHNOLOGY (2007)

Article Biochemical Research Methods

Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data

Nobuyoshi Nagamine et al.

BIOINFORMATICS (2007)

Article Biotechnology & Applied Microbiology

Relating protein pharmacology by ligand chemistry

Michael J. Keiser et al.

NATURE BIOTECHNOLOGY (2007)

Article Biotechnology & Applied Microbiology

Structure-based maximal affinity model predicts small-molecule druggability

Alan C. Cheng et al.

NATURE BIOTECHNOLOGY (2007)

Review Pharmacology & Pharmacy

Chemogenomic approaches to rational drug design

D. Rognan

BRITISH JOURNAL OF PHARMACOLOGY (2007)

Review Pharmacology & Pharmacy

In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling

S. Ekins et al.

BRITISH JOURNAL OF PHARMACOLOGY (2007)

Review Pharmacology & Pharmacy

In silico pharmacology for drug discovery: applications to targets and beyond

S. Ekins et al.

BRITISH JOURNAL OF PHARMACOLOGY (2007)

Review Pharmacology & Pharmacy

Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches

Hanna Eckert et al.

DRUG DISCOVERY TODAY (2007)

Article Chemistry, Medicinal

Graph kernels for molecular structure-activity relationship analysis with support vector machines

P Mahé et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2005)

Article Biochemical Research Methods

Protein homology detection using string alignment kernels

H Saigo et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

The Pfam protein families database

A Bateman et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Chemistry, Multidisciplinary

Comparison of support vector machine and artificial neural network systems for drug/nondrug classification

E Byvatov et al.

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2003)

Article Computer Science, Artificial Intelligence

Training products of experts by minimizing contrastive divergence

GE Hinton

NEURAL COMPUTATION (2002)

Review Pharmacology & Pharmacy

Predicting ADME properties in silico:: methods and models

D Butina et al.

DRUG DISCOVERY TODAY (2002)