The Next Era: Deep Learning in Pharmaceutical Research

Classifying and segmenting microscopy images with deep multiple instance learning

(2016) Oren Z. Kraus et al.   BIOINFORMATICS

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

A renaissance of neural networks in drug discovery

(2016) Igor I. Baskin et al.   Expert Opinion on Drug Discovery

Protein function in precision medicine: deep understanding with machine learning

(2016) Burkhard Rost et al.   FEBS LETTERS

Adapting machine learning techniques to censored time-to-event health record data: A general-purpose approach using inverse probability of censoring weighting

(2016) David M. Vock et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Open Source Bayesian Models. 3. Composite Models for Prediction of Binned Responses

(2016) Alex M. Clark et al.   Journal of Chemical Information and Modeling

Near infrared spectroscopy for counterfeit detection using a large database of pharmaceutical tablets

(2016) Klara Dégardin et al.   JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

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

(2016) Alexander Aliper et al.   MOLECULAR PHARMACEUTICS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

The development of models to predict melting and pyrolysis point data associated with several hundred thousand compounds mined from PATENTS

(2016) Igor V. Tetko et al.   Journal of Cheminformatics

Accurate refinement of docked protein complexes using evolutionary information and deep learning

(2016) Bahar Akbal-Delibas et al.   Journal of Bioinformatics and Computational Biology

Intra- and Inter-Fractional Variation Prediction of Lung Tumors Using Fuzzy Deep Learning

(2016) Seonyeong Park et al.   IEEE Journal of Translational Engineering in Health and Medicine-JTEHM

Computational Intelligence Modeling of the Macromolecules Release from PLGA Microspheres—Focus on Feature Selection

(2016) Hossam M. Zawbaa et al.   PLoS One

Deep Learning in Label-free Cell Classification

(2016) Claire Lifan Chen et al.   Scientific Reports

Machine learning in computational docking

(2015) Mohamed A. Khamis et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Deep convolutional neural networks for annotating gene expression patterns in the mouse brain

(2015) Tao Zeng et al.   BMC BIOINFORMATICS

Computational classification models for predicting the interaction of compounds with hepatic organic ion importers

(2015) Hwan You et al.   Drug Metabolism and Pharmacokinetics

An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions

(2015) Xin Deng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets

(2015) Alex M. Clark et al.   Journal of Chemical Information and Modeling

Open Source Bayesian Models. 2. Mining a “Big Dataset” To Create and Validate Models with ChEMBL

(2015) Alex M. Clark et al.   Journal of Chemical Information and Modeling

Deep Learning for Drug-Induced Liver Injury

(2015) Youjun Xu et al.   Journal of Chemical Information and Modeling

Deep Neural Nets as a Method for Quantitative Structure–Activity Relationships

(2015) Junshui Ma et al.   Journal of Chemical Information and Modeling

Deep Learning in Drug Discovery

(2015) Erik Gawehn et al.   Molecular Informatics

Deep learning

(2015) Yann LeCun et al.   NATURE

A deep learning framework for modeling structural features of RNA-binding protein targets

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Thermodynamic Proxies to Compensate for Biases in Drug Discovery Methods

(2015) Sean Ekins et al.   PHARMACEUTICAL RESEARCH

Modeling and Prediction of Solvent Effect on Human Skin Permeability using Support Vector Regression and Random Forest

(2015) Hiromi Baba et al.   PHARMACEUTICAL RESEARCH

In Silico Estimation of Skin Concentration Following the Dermal Exposure to Chemicals

(2015) Tomomi Hatanaka et al.   PHARMACEUTICAL RESEARCH

Incentives for Starting Small Companies Focused on Rare and Neglected Diseases

(2015) Sean Ekins et al.   PHARMACEUTICAL RESEARCH

In Silico Predictions of Human Skin Permeability using Nonlinear Quantitative Structure–Property Relationship Models

(2015) Hiromi Baba et al.   PHARMACEUTICAL RESEARCH

Developing Enhanced Blood–Brain Barrier Permeability Models: Integrating External Bio-Assay Data in QSAR Modeling

(2015) Wenyi Wang et al.   PHARMACEUTICAL RESEARCH

Predicting Mouse Liver Microsomal Stability with “Pruned” Machine Learning Models and Public Data

(2015) Alexander L. Perryman et al.   PHARMACEUTICAL RESEARCH

Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network

(2015) Tyler B. Hughes et al.   ACS Central Science

Big Data in Chemical Toxicity Research: The Use of High-Throughput Screening Assays To Identify Potential Toxicants

(2014) Hao Zhu et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Are Bigger Data Sets Better for Machine Learning? Fusing Single-Point and Dual-Event Dose Response Data for Mycobacterium tuberculosis

(2014) Sean Ekins et al.   Journal of Chemical Information and Modeling

Bigger data, collaborative tools and the future of predictive drug discovery

(2014) Sean Ekins et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Combining Structure- and Ligand-Based Approaches to Improve Site of Metabolism Prediction in CYP2C9 Substrates

(2014) Laura J. Kingsley et al.   PHARMACEUTICAL RESEARCH

Computational Prediction of Drug Solubility in Fasted Simulated and Aspirated Human Intestinal Fluid

(2014) Jonas H. Fagerberg et al.   PHARMACEUTICAL RESEARCH

Predicting Drug Substances Autoxidation

(2014) P. Lienard et al.   PHARMACEUTICAL RESEARCH

New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0

(2014) Alex M Clark et al.   Journal of Cheminformatics

Machine learning methods in chemoinformatics

(2014) John B. O. Mitchell   Wiley Interdisciplinary Reviews-Computational Molecular Science

Bayesian Models Leveraging Bioactivity and Cytotoxicity Information for Drug Discovery

(2013) Sean Ekins et al.   CHEMISTRY & BIOLOGY

Development of Dimethyl Sulfoxide Solubility Models Using 163 000 Molecules: Using a Domain Applicability Metric to Select More Reliable Predictions

(2013) Igor V. Tetko et al.   Journal of Chemical Information and Modeling

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules

(2013) Alessandro Lusci et al.   Journal of Chemical Information and Modeling

Structure–Activity Relationship for FDA Approved Drugs As Inhibitors of the Human Sodium Taurocholate Cotransporting Polypeptide (NTCP)

(2013) Zhongqi Dong et al.   MOLECULAR PHARMACEUTICS

Computational Models for Neglected Diseases: Gaps and Opportunities

(2013) Elizabeth L. Ponder et al.   PHARMACEUTICAL RESEARCH

Predicting Drug-Target Interactions Using Drug-Drug Interactions

(2013) Shinhyuk Kim et al.   PLoS One

Progress in computational toxicology

(2013) Sean Ekins   JOURNAL OF PHARMACOLOGICAL AND TOXICOLOGICAL METHODS

Deep architectures for protein contact map prediction

(2012) Pietro Di Lena et al.   BIOINFORMATICS

Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation

(2012) Antony J. Williams et al.   DRUG DISCOVERY TODAY

In silico Prediction of Chemical Ames Mutagenicity

(2012) Congying Xu et al.   Journal of Chemical Information and Modeling

Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening

(2012) Liying Zhang et al.   Journal of Chemical Information and Modeling

ADMET Evaluation in Drug Discovery. 12. Development of Binary Classification Models for Prediction of hERG Potassium Channel Blockage

(2012) Sichao Wang et al.   MOLECULAR PHARMACEUTICS

Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches

(2011) Yen Low et al.   CHEMICAL RESEARCH IN TOXICOLOGY

The application of discriminant analysis and Machine Learning methods as tools to identify and classify compounds with potential as transdermal enhancers

(2011) G.P. Moss et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

Binary Classification of Aqueous Solubility Using Support Vector Machines with Reduction and Recombination Feature Selection

(2011) Tiejun Cheng et al.   Journal of Chemical Information and Modeling

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

(2011) Iurii Sushko et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Chembench: a cheminformatics workbench

(2010) Theo Walker et al.   BIOINFORMATICS

A Predictive Ligand-Based Bayesian Model for Human Drug-Induced Liver Injury

(2010) S. Ekins et al.   DRUG METABOLISM AND DISPOSITION

Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research

(2010) Denis Fourches et al.   Journal of Chemical Information and Modeling

Quantitative Structure Activity Relationship for Inhibition of Human Organic Cation/Carnitine Transporter

(2010) Lei Diao et al.   MOLECULAR PHARMACEUTICS

Chemical Space: Missing Pieces in Cheminformatics

(2010) Sean Ekins et al.   PHARMACEUTICAL RESEARCH

Benchmark Data Set for in Silico Prediction of Ames Mutagenicity

(2009) Katja Hansen et al.   Journal of Chemical Information and Modeling

Computational Models for Drug Inhibition of the Human Apical Sodium-Dependent Bile Acid Transporter

(2009) Xiaowan Zheng et al.   MOLECULAR PHARMACEUTICS

New Predictive Models for Blood–Brain Barrier Permeability of Drug-like Molecules

(2008) Sandhya Kortagere et al.   PHARMACEUTICAL RESEARCH