Rethinking drug design in the artificial intelligence era

2018 FDA drug approvals

(2019) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

Prediction of UGT-mediated Metabolism Using the Manually Curated MetaQSAR Database

(2019) Angelica Mazzolari et al.   ACS Medicinal Chemistry Letters

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping

(2019) Boris Sattarov et al.   Journal of Chemical Information and Modeling

Is one-shot learning a viable option in drug discovery?

(2019) Igor I. Baskin   Expert Opinion on Drug Discovery

Automated De Novo Drug Design - “Are we nearly there yet?”

(2019) Gisbert Schneider et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Autonomous Molecular Design: Then and Now

(2019) Tanja Dimitrov et al.   ACS Applied Materials & Interfaces

Biotechnology, Big Data and Artificial Intelligence

(2019) Arlindo L. Oliveira   Biotechnology Journal

Design of Natural‐Product‐Inspired Multitarget Ligands by Machine Learning

(2019) Francesca Grisoni et al.   ChemMedChem

Closing the Loop: Developing an Integrated Design, Make, and Test Platform for Discovery

(2019) David M. Parry   ACS Medicinal Chemistry Letters

Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery

(2019) Xin Yang et al.   CHEMICAL REVIEWS

Enhance Visual Recognition Under Adverse Conditions via Deep Networks

(2019) Ding Liu et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

(2019) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

Adversarial Examples: Attacks and Defenses for Deep Learning

(2019) Xiaoyong Yuan et al.   IEEE Transactions on Neural Networks and Learning Systems

Synthetic Activators of Cell Migration Designed by Constructive Machine Learning

(2019) Dominique Bruns et al.   ChemistryOpen

Machine Learning in Computer-Aided Synthesis Planning

(2018) Connor W. Coley et al.   ACCOUNTS OF CHEMICAL RESEARCH

Artificial Intelligence in Medical Practice: The Question to the Answer?

(2018) D. Douglas Miller et al.   AMERICAN JOURNAL OF MEDICINE

The Molecular Industrial Revolution: Automated Synthesis of Small Molecules

(2018) Melanie Trobe et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Practical application of ligand efficiency metrics in lead optimisation

(2018) James S. Scott et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Challenges with multi-objective QSAR in drug discovery

(2018) George Lambrinidis et al.   Expert Opinion on Drug Discovery

DNA-encoded chemical libraries - achievements and remaining challenges

(2018) Nicholas Favalli et al.   FEBS LETTERS

Design, Synthesis, and Testing of Potent, Selective Hepsin Inhibitors via Application of an Automated Closed-Loop Optimization Platform

(2018) Shishir M. Pant et al.   JOURNAL OF MEDICINAL CHEMISTRY

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

Generative Models for Artificially-intelligent Molecular Design

(2018) Gisbert Schneider   Molecular Informatics

De Novo Design of Bioactive Small Molecules by Artificial Intelligence

(2018) Daniel Merk et al.   Molecular Informatics

Organic synthesis provides opportunities to transform drug discovery

(2018) David C. Blakemore et al.   Nature Chemistry

“Found in Translation”: predicting outcomes of complex organic chemistry reactions using neural sequence-to-sequence models

(2018) Philippe Schwaller et al.   Chemical Science

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

(2018) Rafael Gómez-Bombarelli et al.   ACS Central Science

Review of diagnostic error in anatomical pathology and the role and value of second opinions in error prevention

(2018) Martyn Peck et al.   JOURNAL OF CLINICAL PATHOLOGY

Data Curation can Improve the Prediction Accuracy of Metabolic Intrinsic Clearance

(2018) Tsuyoshi Esaki et al.   Molecular Informatics

AI could threaten pharmaceutical patents

(2018) Lutz Heuer   NATURE

Nanoscale synthesis and affinity ranking

(2018) Nathan J. Gesmundo et al.   NATURE

Dilemma over AI and drug patenting already under debate

(2018) Ross D. King et al.   NATURE

Planning chemical syntheses with deep neural networks and symbolic AI

(2018) Marwin H. S. Segler et al.   NATURE

Expanding the medicinal chemistry synthetic toolbox

(2018) Jonas Boström et al.   NATURE REVIEWS DRUG DISCOVERY

Reconfigurable system for automated optimization of diverse chemical reactions

(2018) Anne-Catherine Bédard et al.   SCIENCE

Deep reinforcement learning for de novo drug design

(2018) Mariya Popova et al.   Science Advances

Guest Editorial: Critical Thinking in Education and Research-Why and How?

(2018) Norman Sieroka et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Advances in Lead Generation

(2018) Joerg Holenz et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

An approach towards enhancement of a screening library: The Next Generation Library Initiative (NGLI) at Bayer — against all odds?

(2018) Markus Follmann et al.   DRUG DISCOVERY TODAY

Artificial Intelligence in Drug Design

(2018) Gerhard Hessler et al.   MOLECULES

High-performance medicine: the convergence of human and artificial intelligence

(2018) Eric J. Topol   NATURE MEDICINE

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Deep neural network improves fracture detection by clinicians

(2018) Robert Lindsey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organic synthesis in a modular robotic system driven by a chemical programming language

(2018) Sebastian Steiner et al.   SCIENCE

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

(2018) Allan M. Jordan   ACS Medicinal Chemistry Letters

Ligand efficiency metrics in drug discovery: the pros and cons from a practical perspective

(2017) Maria Maddalena Cavalluzzi et al.   Expert Opinion on Drug Discovery

Extending ‘predict first’ to the design-make-test cycle in small-molecule drug discovery

(2017) Scott Harrison et al.   Future Medicinal Chemistry

Active learning for computational chemogenomics

(2017) Daniel Reker et al.   Future Medicinal Chemistry

Topliss Batchwise Schemes Reviewed in the Era of Open Data Reveal Significant Differences between Enzymes and Membrane Receptors

(2017) Lars Richter   Journal of Chemical Information and Modeling

Chemical Space Mimicry for Drug Discovery

(2017) William Yuan et al.   Journal of Chemical Information and Modeling

Generative Recurrent Networks for De Novo Drug Design

(2017) Anvita Gupta et al.   Molecular Informatics

Application of Generative Autoencoder in De Novo Molecular Design

(2017) Thomas Blaschke et al.   Molecular Informatics

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

(2017) Alexandru Korotcov et al.   MOLECULAR PHARMACEUTICS

Automating drug discovery

(2017) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Applications of chemogenomic library screening in drug discovery

(2017) Lyn H. Jones et al.   NATURE REVIEWS DRUG DISCOVERY

Opportunities and challenges in phenotypic drug discovery: an industry perspective

(2017) John G. Moffat et al.   NATURE REVIEWS DRUG DISCOVERY

Deriving genomic diagnoses without revealing patient genomes

(2017) Karthik A. Jagadeesh et al.   SCIENCE

High-Throughput Automation in Chemical Process Development

(2017) Joshua A. Selekman et al.   Annual Review of Chemical and Biomolecular Engineering

Integrated Platform for Expedited Synthesis–Purification–Testing of Small Molecule Libraries

(2017) Aleksandra Baranczak et al.   ACS Medicinal Chemistry Letters

HEp-2 Cell Image Classification With Deep Convolutional Neural Networks

(2017) Zhimin Gao et al.   IEEE Journal of Biomedical and Health Informatics

Drug target ontology to classify and integrate drug discovery data

(2017) Yu Lin et al.   Journal of Biomedical Semantics

Low Data Drug Discovery with One-Shot Learning

(2017) Han Altae-Tran et al.   ACS Central Science

Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks

(2017) Marwin H. S. Segler et al.   ACS Central Science

Computer-Assisted Synthetic Planning: The End of the Beginning

(2016) Sara Szymkuć et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Cell-Specific Computational Modeling of the PIM Pathway in Acute Myeloid Leukemia

(2016) Dana Silverbush et al.   CANCER RESEARCH

Improving Drug Design: An Update on Recent Applications of Efficiency Metrics, Strategies for Replacing Problematic Elements, and Compounds in Nontraditional Drug Space

(2016) Nicholas A. Meanwell   CHEMICAL RESEARCH IN TOXICOLOGY

Computer Aided Drug Design: Success and Limitations

(2016) Mohammad Hassan Baig et al.   CURRENT PHARMACEUTICAL DESIGN

Stuck in a rut with old chemistry

(2016) Jonas Boström et al.   DRUG DISCOVERY TODAY

Why and how have drug discovery strategies in pharma changed? What are the new mindsets?

(2016) Serge Mignani et al.   DRUG DISCOVERY TODAY

Extending accessible chemical space for the identification of novel leads

(2016) Jürgen Bajorath   Expert Opinion on Drug Discovery

Macromolecular target prediction by self-organizing feature maps

(2016) Gisbert Schneider et al.   Expert Opinion on Drug Discovery

A Primer on Neural Network Models for Natural Language Processing

(2016) Yoav Goldberg   JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH

Inverse QSPR/QSAR Analysis for Chemical Structure Generation (from y to x)

(2016) Tomoyuki Miyao et al.   Journal of Chemical Information and Modeling

Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation

(2016) Denis Fourches et al.   Journal of Chemical Information and Modeling

Chemical Space of DNA-Encoded Libraries

(2016) Raphael M. Franzini et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2016) Alexander Aliper et al.   MOLECULAR PHARMACEUTICS

Trends in clinical success rates

(2016) Katarzyna Smietana et al.   NATURE REVIEWS DRUG DISCOVERY

A comprehensive map of molecular drug targets

(2016) Rita Santos et al.   NATURE REVIEWS DRUG DISCOVERY

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

Multi-objective active machine learning rapidly improves structure–activity models and reveals new protein–protein interaction inhibitors

(2016) D. Reker et al.   Chemical Science

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

(2016) Ruili Huang et al.   Nature Communications

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Drug Discovery Goes Three-Dimensional: Goodbye to Flat High-Throughput Screening?

(2015) Richard M. Eglen et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

Quantitative high-throughput screening data analysis: challenges and recent advances

(2015) Keith R. Shockley   DRUG DISCOVERY TODAY

The Purchasable Chemical Space: A Detailed Picture

(2015) Xavier Lucas et al.   Journal of Chemical Information and Modeling

Activity, assay and target data curation and quality in the ChEMBL database

(2015) George Papadatos et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Deep learning

(2015) Yann LeCun et al.   NATURE

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Predicting drug metabolism: experiment and/or computation?

(2015) Johannes Kirchmair et al.   NATURE REVIEWS DRUG DISCOVERY

Organs-on-chips at the frontiers of drug discovery

(2015) Eric W. Esch et al.   NATURE REVIEWS DRUG DISCOVERY

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

FutureTox II: In vitro Data and In Silico Models for Predictive Toxicology

(2015) Thomas B. Knudsen et al.   TOXICOLOGICAL SCIENCES

Quantitative in vitro-to-in vivo extrapolation in a high-throughput environment

(2015) Barbara A. Wetmore   TOXICOLOGY

A reliable computational workflow for the selection of optimal screening libraries

(2015) Yocheved Gilad et al.   Journal of Cheminformatics

Multidimensional De Novo Design Reveals 5-HT2BReceptor-Selective Ligands

(2014) Tiago Rodrigues et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Multi-Objective Molecular De Novo Design by Adaptive Fragment Prioritization

(2014) Michael Reutlinger et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Is target validation all we need?

(2014) Melanie M Frigault et al.   CURRENT OPINION IN PHARMACOLOGY

The eTOX Data-Sharing Project to Advance in Silico Drug-Induced Toxicity Prediction

(2014) Montserrat Cases et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Uniting Cheminformatics and Chemical Theory To Predict the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules

(2014) James L. McDonagh et al.   Journal of Chemical Information and Modeling

Ligand efficiency metrics considered harmful

(2014) Peter W. Kenny et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structural Mechanisms Determining Inhibition of the Collagen Receptor DDR1 by Selective and Multi-Targeted Type II Kinase Inhibitors

(2014) Peter Canning et al.   JOURNAL OF MOLECULAR BIOLOGY

The role of ligand efficiency metrics in drug discovery

(2014) Andrew L. Hopkins et al.   NATURE REVIEWS DRUG DISCOVERY

Scientific competency questions as the basis for semantically enriched open pharmacological space development

(2013) Kamal Azzaoui et al.   DRUG DISCOVERY TODAY

Data-driven medicinal chemistry in the era of big data

(2013) Scott J. Lusher et al.   DRUG DISCOVERY TODAY

Chemical predictive modelling to improve compound quality

(2013) John G. Cumming et al.   NATURE REVIEWS DRUG DISCOVERY

Comparability of Mixed IC50 Data – A Statistical Analysis

(2013) Tuomo Kalliokoski et al.   PLoS One

Multi-Parameter Optimization: Identifying High Quality Compounds with a Balance of Properties

(2012) Matthew D. Segall   CURRENT PHARMACEUTICAL DESIGN

Multi-Objective Optimization with Estimation of Distribution Algorithm in a Noisy Environment

(2012) Vui Ann Shim et al.   EVOLUTIONARY COMPUTATION

DOGS: Reaction-Driven de novo Design of Bioactive Compounds

(2012) Markus Hartenfeller et al.   PLoS Computational Biology

Hypothesis driven drug design: improving quality and effectiveness of the design-make-test-analyse cycle

(2011) Alleyn T. Plowright et al.   DRUG DISCOVERY TODAY

Strategies of multi-objective optimization in drug discovery and development

(2011) Orazio Nicolotti et al.   Expert Opinion on Drug Discovery

Medicinal chemistry for 2020

(2011) Seetharama D Satyanarayanajois et al.   Future Medicinal Chemistry

Matched Molecular Pairs as a Medicinal Chemistry Tool

(2011) Ed Griffen et al.   JOURNAL OF MEDICINAL CHEMISTRY

The Medicinal Chemist’s Toolbox: An Analysis of Reactions Used in the Pursuit of Drug Candidates

(2011) Stephen D. Roughley et al.   JOURNAL OF MEDICINAL CHEMISTRY

Size estimation of chemical space: how big is it?

(2011) Kurt L. M. Drew et al.   JOURNAL OF PHARMACY AND PHARMACOLOGY

Evolving molecules using multi-objective optimization: applying to ADME/Tox

(2010) Sean Ekins et al.   DRUG DISCOVERY TODAY

De novodesign: balancing novelty and confined chemical space

(2010) Peter S Kutchukian et al.   Expert Opinion on Drug Discovery

How to improve R&D productivity: the pharmaceutical industry's grand challenge

(2010) Steven M. Paul et al.   NATURE REVIEWS DRUG DISCOVERY

Chemical space as a source for new drugs

(2010) Jean-Louis Reymond et al.   MedChemComm

Novel trends in high-throughput screening

(2009) Lorenz M Mayr et al.   CURRENT OPINION IN PHARMACOLOGY

Drug discovery chemistry: a primer for the non-specialist

(2009) Allan M. Jordan et al.   DRUG DISCOVERY TODAY

Making medicinal chemistry more effective—application of Lean Sigma to improve processes, speed and quality

(2009) Shalini Andersson et al.   DRUG DISCOVERY TODAY

Target discovery from data mining approaches

(2009) Yongliang Yang et al.   DRUG DISCOVERY TODAY

Healthy skepticism: assessing realistic model performance

(2009) Scott P. Brown et al.   DRUG DISCOVERY TODAY

Make Way for Robot Scientists

(2009) R. D. King et al.   SCIENCE

The Automation of Science

(2009) Ross D. King et al.   SCIENCE

A constructive approach for discovering new drug leads: Using a kernel methodology for the inverse-QSAR problem

(2009) William WL Wong et al.   Journal of Cheminformatics

Molecule-pharmacophore superpositioning and pattern matching in computational drug design

(2007) G WOLBER   DRUG DISCOVERY TODAY