Artificial intelligence in the early stages of drug discovery

A Deep Learning Approach to Antibiotic Discovery

(2020) Jonathan M. Stokes et al.   CELL

Reply to ‘Assessing the impact of generative AI on medicinal chemistry’

(2020) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

Assessing the impact of generative AI on medicinal chemistry

(2020) W. Patrick Walters et al.   NATURE BIOTECHNOLOGY

De novo generation of hit-like molecules from gene expression signatures using artificial intelligence

(2020) Oscar Méndez-Lucio et al.   Nature Communications

Deep Generative Models for 3D Linker Design

(2020) Fergus Imrie et al.   Journal of Chemical Information and Modeling

Fast Rescoring Protocols to Improve the Performance of Structure-Based Virtual Screening Performed on Protein–Protein Interfaces

(2020) Natesh Singh et al.   Journal of Chemical Information and Modeling

Machine learning classification can reduce false positives in structure-based virtual screening

(2020) Yusuf O. Adeshina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches

(2020) Javier Vázquez et al.   MOLECULES

Predictive Multitask Deep Neural Network Models for ADME-Tox Properties: Learning from Large Datasets

(2019) Jan Wenzel et al.   Journal of Chemical Information and Modeling

BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design

(2019) William Farnaby et al.   Nature Chemical Biology

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

(2019) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

(2019) Pin Chen et al.   Journal of Cheminformatics

A Bayesian machine learning approach for drug target identification using diverse data types

(2019) Neel S. Madhukar et al.   Nature Communications

Estimation of clinical trial success rates and related parameters

(2018) Chi Heem Wong et al.   BIOSTATISTICS

The rise of deep learning in drug discovery

(2018) Hongming Chen et al.   DRUG DISCOVERY TODAY

Fragment-Based Approach to Targeting Inosine-5′-monophosphate Dehydrogenase (IMPDH) from Mycobacterium tuberculosis

(2018) Ana Trapero et al.   JOURNAL OF MEDICINAL CHEMISTRY

Deep Generative Models for Molecular Science

(2018) Peter B. Jørgensen et al.   Molecular Informatics

MoleculeNet: a benchmark for molecular machine learning

(2018) Zhenqin Wu et al.   Chemical Science

A confidence predictor for logD using conformal regression and a support-vector machine

(2018) Maris Lapins et al.   Journal of Cheminformatics

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

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

In Silico Prediction of Chemical Toxicity for Drug Design Using Machine Learning Methods and Structural Alerts

(2018) Hongbin Yang et al.   Frontiers in Chemistry

Development of a Protein-Ligand Extended Connectivity (PLEC) fingerprint and its application for binding affinity predictions

(2018) Maciej Wójcikowski et al.   BIOINFORMATICS

Computational chemistry in drug lead discovery and design

(2018) Claudio N. Cavasotto et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Multi-objective de novo drug design with conditional graph generative model

(2018) Yibo Li et al.   Journal of Cheminformatics

Artificial intelligence in drug development: present status and future prospects

(2018) Kit-Kay Mak et al.   DRUG DISCOVERY TODAY

Deep learning and virtual drug screening

(2018) Kristy A Carpenter et al.   Future Medicinal Chemistry

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

In silico prediction of novel therapeutic targets using gene–disease association data

(2017) Enrico Ferrero et al.   Journal of Translational Medicine

Application of Generative Autoencoder in De Novo Molecular Design

(2017) Thomas Blaschke et al.   Molecular Informatics

The Drug Repurposing Hub: a next-generation drug library and information resource

(2017) Steven M Corsello et al.   NATURE MEDICINE

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set

(2017) Eelke B. Lenselink et al.   Journal of Cheminformatics

ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

(2017) Jiangming Sun et al.   Journal of Cheminformatics

Molecular de-novo design through deep reinforcement learning

(2017) Marcus Olivecrona et al.   Journal of Cheminformatics

vNN Web Server for ADMET Predictions

(2017) Patric Schyman et al.   Frontiers in Pharmacology

Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks

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

Performance of machine-learning scoring functions in structure-based virtual screening

(2017) Maciej Wójcikowski et al.   Scientific Reports

I. Discovery of a novel series of CXCR3 antagonists. Multiparametric optimization of N , N -disubstituted benzylamines

(2016) Imre Bata et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Optimised method to estimate octanol water distribution coefficient (logD) in a high throughput format

(2016) Ying Wei (Ivan) Low et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

Boosting Docking-Based Virtual Screening with Deep Learning

(2016) Janaina Cruz Pereira et al.   Journal of Chemical Information and Modeling

Innovation in the pharmaceutical industry: New estimates of R&D costs

(2016) Joseph A. DiMasi et al.   JOURNAL OF HEALTH ECONOMICS

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

(2016) Alexander Aliper et al.   MOLECULAR PHARMACEUTICS

Open Targets: a platform for therapeutic target identification and validation

(2016) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology

(2016) Artur Kadurin et al.   Oncotarget

Recent progresses in the exploration of machine learning methods as in-silico ADME prediction tools

(2015) L. Tao et al.   ADVANCED DRUG DELIVERY REVIEWS

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description

(2015) Francesca Spyrakis et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Toxicology Strategies for Drug Discovery: Present and Future

(2015) Eric A. G. Blomme et al.   CHEMICAL RESEARCH IN TOXICOLOGY

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

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets

(2015) Hongjian Li et al.   Molecular Informatics

A Generally Applicable Computer Algorithm Based on the Group Additivity Method for the Calculation of Seven Molecular Descriptors: Heat of Combustion, LogPO/W, LogS, Refractivity, Polarizability, Toxicity and LogBB of Organic Compounds; Scope and Limits of Applicability

(2015) Rudolf Naef   MOLECULES

Pharmacophore Models and Pharmacophore-Based Virtual Screening: Concepts and Applications Exemplified on Hydroxysteroid Dehydrogenases

(2015) Teresa Kaserer et al.   MOLECULES

Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions

(2015) Andrea Bazzoli et al.   PLoS One

Critical role of c-jun N-terminal protein kinase in promoting mitochondrial dysfunction and acute liver injury

(2015) Sehwan Jang et al.   Redox Biology

Applying machine learning techniques for ADME-Tox prediction: a review

(2014) Vinícius Gonçalves Maltarollo et al.   Expert Opinion on Drug Metabolism & Toxicology

Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

(2014) Pedro J. Ballester et al.   Journal of Chemical Information and Modeling

Improvement of Virtual Screening Results by Docking Data Feature Analysis

(2014) Marcelino Arciniega et al.   Journal of Chemical Information and Modeling

Beware of Machine Learning-Based Scoring Functions—On the Danger of Developing Black Boxes

(2014) Joffrey Gabel et al.   Journal of Chemical Information and Modeling

Structural Protein–Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study

(2014) C. Da et al.   Journal of Chemical Information and Modeling

SAMPL4 & DOCK3.7: lessons for automated docking procedures

(2014) Ryan G. Coleman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

ADMET Evaluation in Drug Discovery. 13. Development of in Silico Prediction Models for P-Glycoprotein Substrates

(2014) Dan Li et al.   MOLECULAR PHARMACEUTICS

A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening

(2014) Jouhyun Jeon et al.   Genome Medicine

Quantum chemistry structures and properties of 134 kilo molecules

(2014) Raghunathan Ramakrishnan et al.   Scientific Data

Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data

(2014) Anton A. Buzdin et al.   Frontiers in Genetics

Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening

(2013) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets

(2013) Matthias R. Bauer et al.   Journal of Chemical Information and Modeling

Chemical predictive modelling to improve compound quality

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

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

PubChem BioAssay: 2014 update

(2013) Yanli Wang et al.   NUCLEIC ACIDS RESEARCH

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

Correction: Analysis of Unannotated Equine Transcripts Identified by mRNA Sequencing

(2013) Stephen J. Coleman et al.   PLoS One

Open-source platform to benchmark fingerprints for ligand-based virtual screening

(2013) Sereina Riniker et al.   Journal of Cheminformatics

CancerDR: Cancer Drug Resistance Database

(2013) Rahul Kumar et al.   Scientific Reports

The Future of Virtual Compound Screening

(2012) Kathrin Heikamp et al.   Chemical Biology & Drug Design

Locally Weighted Learning Methods for Predicting Dose-Dependent Toxicity with Application to the Human Maximum Recommended Daily Dose

(2012) Ruifeng Liu et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Oxidant stress, mitochondria, and cell death mechanisms in drug-induced liver injury: Lessons learned from acetaminophen hepatotoxicity

(2012) Hartmut Jaeschke et al.   DRUG METABOLISM REVIEWS

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

Surflex-Dock: Docking benchmarks and real-world application

(2012) Russell Spitzer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

FRED and HYBRID docking performance on standardized datasets

(2012) Mark McGann   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Docking and scoring with ICM: the benchmarking results and strategies for improvement

(2012) Marco A. C. Neves et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

The enumeration of chemical space

(2012) Jean-Louis Reymond et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Structure-based optimization of potent 4- and 6-azaindole-3-carboxamides as renin inhibitors

(2011) Bodo Scheiper et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Structure-based design and optimization of potent renin inhibitors on 5- or 7-azaindole-scaffolds

(2011) Hans Matter et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

FDA-approved drug labeling for the study of drug-induced liver injury

(2011) Minjun Chen et al.   DRUG DISCOVERY TODAY

DEKOIS: Demanding Evaluation Kits for Objectivein SilicoScreening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions

(2011) Simon M. Vogel et al.   Journal of Chemical Information and Modeling

A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing

(2011) Sarah L. Kinnings et al.   Journal of Chemical Information and Modeling

NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function

(2011) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

Mixed learning algorithms and features ensemble in hepatotoxicity prediction

(2011) Chin Yee Liew et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Qualitative prediction of blood–brain barrier permeability on a large and refined dataset

(2011) Markus Muehlbacher et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A Novel Approach for Predicting P-Glycoprotein (ABCB1) Inhibition Using Molecular Interaction Fields

(2011) Fabio Broccatelli et al.   JOURNAL OF MEDICINAL CHEMISTRY

BINANA: A novel algorithm for ligand-binding characterization

(2011) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

ADME Evaluation in Drug Discovery. 10. Predictions of P-Glycoprotein Inhibitors Using Recursive Partitioning and Naive Bayesian Classification Techniques

(2011) Lei Chen et al.   MOLECULAR PHARMACEUTICS

Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells

(2011) Richard Marcotte et al.   Cancer Discovery

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

Discovery and optimization of a new class of potent and non-chiral indole-3-carboxamide-based renin inhibitors

(2010) Bodo Scheiper et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Discovery of a novel series of CXCR3 antagonists

(2010) Stefano Crosignani et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Principles of early drug discovery

(2010) JP Hughes et al.   BRITISH JOURNAL OF PHARMACOLOGY

Developing Structure−Activity Relationships for the Prediction of Hepatotoxicity

(2010) Nigel Greene et al.   CHEMICAL RESEARCH IN TOXICOLOGY

PubChem as a public resource for drug discovery

(2010) Qingliang Li et al.   DRUG DISCOVERY TODAY

Extended-Connectivity Fingerprints

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

A high throughput dried DMSO LogD lipophilicity measurement based on 96-well shake-flask and atmospheric pressure photoionization mass spectrometry detection

(2010) Yun W. Alelyunas et al.   JOURNAL OF CHROMATOGRAPHY A

PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints

(2010) Chun Wei Yap   JOURNAL OF COMPUTATIONAL CHEMISTRY

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

(2009) L. Xie et al.   BIOINFORMATICS

Properties and identification of human protein drug targets

(2009) Tala M. Bakheet et al.   BIOINFORMATICS

High-throughput andin silicoscreenings in drug discovery

(2009) Sharangdhar S Phatak et al.   Expert Opinion on Drug Discovery

Structure-Activity Relationships and X-ray Structures Describing the Selectivity of Aminopyrazole Inhibitors for c-Jun N-terminal Kinase 3 (JNK3) over p38

(2009) Ted Kamenecka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening

(2009) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

(2009) Jason B. Cross et al.   Journal of Chemical Information and Modeling

Benchmark Data Set for in Silico Prediction of Ames Mutagenicity

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

Design, Synthesis, and Structure−Activity Relationship of Substrate Competitive, Selective, and in Vivo Active Triazole and Thiadiazole Inhibitors of the c-Jun N-Terminal Kinase

(2009) Surya K. De et al.   JOURNAL OF MEDICINAL CHEMISTRY

PubChem BioAssays as a data source for predictive models

(2009) Bin Chen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

DOCK 6: Combining techniques to model RNA-small molecule complexes

(2009) P. T. Lang et al.   RNA

Drug-induced liver injury through mitochondrial dysfunction: mechanisms and detection during preclinical safety studies

(2008) Gilles Labbe et al.   FUNDAMENTAL & CLINICAL PHARMACOLOGY

Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization

(2008) Fabian Dey et al.   Journal of Chemical Information and Modeling

Mold2, Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics

(2008) Huixiao Hong et al.   Journal of Chemical Information and Modeling

CONFIRM: connecting fragments found in receptor molecules

(2008) David C. Thompson et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellular Imaging Predictions of Clinical Drug-Induced Liver Injury

(2008) Jinghai J. Xu et al.   TOXICOLOGICAL SCIENCES