The challenges of generalizability in artificial intelligence for ADME/Tox endpoint and activity prediction

A Deep Learning Approach to Antibiotic Discovery

(2020) Jonathan M. Stokes et al.   CELL

Exploring chemical space using natural language processing methodologies for drug discovery

(2020) Hakime Öztürk et al.   DRUG DISCOVERY TODAY

Image Based Liver Toxicity Prediction

(2020) Ece Asilar et al.   Journal of Chemical Information and Modeling

Tapping on the Black Box: How Is the Scoring Power of a Machine-Learning Scoring Function Dependent on the Training Set?

(2020) Minyi Su et al.   Journal of Chemical Information and Modeling

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

The unreasonable effectiveness of deep learning in artificial intelligence

(2020) Terrence J. Sejnowski   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Throughput Screening to Predict Chemical-Assay Interference

(2020) Alexandre Borrel et al.   Scientific Reports

Practical Applications of Deep Learning to Impute Heterogeneous Drug Discovery Data

(2020) Benedict Irwin et al.   Journal of Chemical Information and Modeling

Artificial intelligence in chemistry and drug design

(2020) Nathan Brown et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis

(2020) Thomas J. Struble et al.   JOURNAL OF MEDICINAL CHEMISTRY

Learning Molecular Representations for Medicinal Chemistry

(2020) Kangway V. Chuang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Improvement in ADMET Prediction with Multitask Deep Featurization

(2020) Evan N. Feinberg et al.   JOURNAL OF MEDICINAL CHEMISTRY

How We Think about Targeting RNA with Small Molecules

(2020) Matthew G. Costales et al.   JOURNAL OF MEDICINAL CHEMISTRY

What makes a drug discovery consortium successful?

(2020) Peter B. Simpson et al.   NATURE REVIEWS DRUG DISCOVERY

Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT

(2020) Xinhao Li et al.   Journal of Cheminformatics

Uncertainty Quantification Using Neural Networks for Molecular Property Prediction

(2020) Lior Hirschfeld et al.   Journal of Chemical Information and Modeling

Transfer Learning for Drug Discovery

(2020) Chenjing Cai et al.   JOURNAL OF MEDICINAL CHEMISTRY

Accelerating Therapeutics for Opportunities in Medicine: A Paradigm Shift in Drug Discovery

(2020) Izumi V. Hinkson et al.   Frontiers in Pharmacology

Molecular representations in AI-driven drug discovery: a review and practical guide

(2020) Laurianne David et al.   Journal of Cheminformatics

Comparative study between deep learning and QSAR classifications for TNBC inhibitors and novel GPCR agonist discovery

(2020) Lun K. Tsou et al.   Scientific Reports

Applications of Deep Learning in Molecule Generation and Molecular Property Prediction

(2020) W. Patrick Walters et al.   ACCOUNTS OF CHEMICAL RESEARCH

‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures

(2020) Ewen Callaway   NATURE

Exploiting machine learning for end-to-end drug discovery and development

(2019) Sean Ekins et al.   NATURE MATERIALS

Applications of machine learning in drug discovery and development

(2019) Jessica Vamathevan et al.   NATURE REVIEWS DRUG DISCOVERY

Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery

(2019) Xin Yang et al.   CHEMICAL REVIEWS

Neural networks in drug discovery: current insights from medicinal chemists

(2019) Yinqiu Xu et al.   Future Medicinal Chemistry

Analyzing Learned Molecular Representations for Property Prediction

(2019) Kevin Yang et al.   Journal of Chemical Information and Modeling

Three pitfalls to avoid in machine learning

(2019) Patrick Riley   NATURE

Big Data and Artificial Intelligence Modeling for Drug Discovery

(2019) Hao Zhu   Annual Review of Pharmacology and Toxicology

Molecular Transformer: A Model for Uncertainty-Calibrated Chemical Reaction Prediction

(2019) Philippe Schwaller et al.   ACS Central Science

Deep Transferable Compound Representation across Domains and Tasks for Low Data Drug Discovery

(2019) Karim Abbasi et al.   Journal of Chemical Information and Modeling

Hunting for New Drugs with AI

(2019) David H. Freedman   NATURE

Rethinking drug design in the artificial intelligence era

(2019) Petra Schneider et al.   NATURE REVIEWS DRUG DISCOVERY

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

Machine learning in chemoinformatics and drug discovery

(2018) Yu-Chen Lo et al.   DRUG DISCOVERY TODAY

Large-scale comparison of machine learning methods for drug target prediction on ChEMBL

(2018) Andreas Mayr et al.   Chemical Science

MoleculeNet: a benchmark for molecular machine learning

(2018) Zhenqin Wu et al.   Chemical Science

Dissecting Machine-Learning Prediction of Molecular Activity: Is an Applicability Domain Needed for Quantitative Structure–Activity Relationship Models Based on Deep Neural Networks?

(2018) Ruifeng Liu et al.   Journal of Chemical Information and Modeling

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Artificial Intelligence in Drug Design—The Storm Before the Calm?

(2018) Allan M. Jordan   ACS Medicinal Chemistry Letters

PotentialNet for Molecular Property Prediction

(2018) Evan N. Feinberg et al.   ACS Central Science

Is Multitask Deep Learning Practical for Pharma?

(2017) Bharath Ramsundar et al.   Journal of Chemical Information and Modeling

Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction

(2017) Connor W. Coley et al.   Journal of Chemical Information and Modeling

Meta-QSAR: a large-scale application of meta-learning to drug design and discovery

(2017) Ivan Olier et al.   MACHINE LEARNING

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

(2017) Alexandru Korotcov et al.   MOLECULAR PHARMACEUTICS

Quantum-chemical insights from deep tensor neural networks

(2017) Kristof T. Schütt et al.   Nature Communications

Efficiency of different measures for defining the applicability domain of classification models

(2017) Waldemar Klingspohn et al.   Journal of Cheminformatics

Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data

(2017) Alexios Koutsoukas et al.   Journal of Cheminformatics

Hybridizing Feature Selection and Feature Learning Approaches in QSAR Modeling for Drug Discovery

(2017) Ignacio Ponzoni et al.   Scientific Reports

Chemoinformatic Classification Methods and their Applicability Domain

(2016) Miriam Mathea et al.   Molecular Informatics

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

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

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

Deep learning

(2015) Yann LeCun et al.   NATURE

Applicability Domain Analysis (ADAN): A Robust Method for Assessing the Reliability of Drug Property Predictions

(2014) Pau Carrió et al.   Journal of Chemical Information and Modeling

The application of conformal prediction to the drug discovery process

(2013) Martin Eklund et al.   ANNALS OF MATHEMATICS AND ARTIFICIAL INTELLIGENCE

How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space

(2013) Alexios Koutsoukas 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

Time-Split Cross-Validation as a Method for Estimating the Goodness of Prospective Prediction.

(2013) Robert P. Sheridan   Journal of Chemical Information and Modeling

QSAR Modeling: Where Have You Been? Where Are You Going To?

(2013) Artem Cherkasov et al.   JOURNAL OF MEDICINAL CHEMISTRY

ChEMBL: a large-scale bioactivity database for drug discovery

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

Extended-Connectivity Fingerprints

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

Mining large heterogeneous data sets in drug discovery

(2009) David J Wild   Expert Opinion on Drug Discovery

A Survey on Transfer Learning

(2009) Sinno Jialin Pan et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space

(2009) Andreas Bender et al.   Journal of Chemical Information and Modeling

How not to develop a quantitative structure–activity or structure–property relationship (QSAR/QSPR)

(2009) J.C. Dearden et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH