Generative chemistry: drug discovery with deep learning generative models

Estimated Research and Development Investment Needed to Bring a New Medicine to Market, 2009-2018

(2020) Olivier J. Wouters et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

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

Mol-CycleGAN: a generative model for molecular optimization

(2020) Łukasz Maziarka et al.   Journal of Cheminformatics

The Synthesizability of Molecules Proposed by Generative Models

(2020) Wenhao Gao et al.   Journal of Chemical Information and Modeling

Deep Generative Models for 3D Linker Design

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

Discovery of Orally Bioavailable Chromone Derivatives as Potent and Selective BRD4 Inhibitors: Scaffold Hopping, Optimization, and Pharmacological Evaluation

(2020) Zhiqing Liu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Comparing Machine Learning Algorithms for Predicting Drug-Induced Liver Injury (DILI)

(2020) Eni Minerali et al.   MOLECULAR PHARMACEUTICS

Molecular Generation for Desired Transcriptome Changes With Adversarial Autoencoders

(2020) Rim Shayakhmetov et al.   Frontiers in Pharmacology

Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research

(2020) Zhiwei Feng et al.   BRIEFINGS IN BIOINFORMATICS

Advances in G protein-coupled receptor high-throughput screening

(2020) Emily A. Yasi et al.   CURRENT OPINION IN BIOTECHNOLOGY

High-Throughput Screening: today’s biochemical and cell-based approaches

(2020) Vincent Blay et al.   DRUG DISCOVERY TODAY

Pain-CKB, A Pain Domain-specific Chemogenomics Knowledgebase for Target Identification and Systems Pharmacology Research

(2020) Zhiwei Feng et al.   Journal of Chemical Information and Modeling

Deep Reinforcement Learning for Multiagent Systems: A Review of Challenges, Solutions, and Applications

(2020) Thanh Thi Nguyen et al.   IEEE Transactions on Cybernetics

The integration of pharmacophore-based 3D QSAR modeling and virtual screening in safety profiling: A case study to identify antagonistic activities against adenosine receptor, A2A, using 1,897 known drugs

(2019) Fan Fan et al.   PLoS One

QBMG: quasi-biogenic molecule generator with deep recurrent neural network

(2019) Shuangjia Zheng et al.   Journal of Cheminformatics

Significantly different effects of tetrahydroberberrubine enantiomers on dopamine D1/D2 receptors revealed by experimental study and integrated in silico simulation

(2019) Haixia Ge et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Deep learning for molecular generation

(2019) Youjun Xu et al.   Future Medicinal Chemistry

Prediction of Orthosteric and Allosteric Regulations on Cannabinoid Receptors Using Supervised Machine Learning Classifiers

(2019) Yuemin Bian et al.   MOLECULAR PHARMACEUTICS

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

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

(2019) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

Investigation of Machine Intelligence in Compound Cell Activity Classification

(2019) Yuanrong Fan et al.   MOLECULAR PHARMACEUTICS

Deep Convolutional Generative Adversarial Network (dcGAN) Models for Screening and Design of Small Molecules Targeting Cannabinoid Receptors

(2019) Yuemin Bian et al.   MOLECULAR PHARMACEUTICS

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

A de novo molecular generation method using latent vector based generative adversarial network

(2019) Oleksii Prykhodko et al.   Journal of Cheminformatics

Computational Fragment-Based Drug Design: Current Trends, Strategies, and Applications

(2018) Yuemin Bian et al.   AAPS Journal

Deep Learning for Drug Design: an Artificial Intelligence Paradigm for Drug Discovery in the Big Data Era

(2018) Yankang Jing et al.   AAPS Journal

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

Machine learning in chemoinformatics and drug discovery

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

SCScore: Synthetic Complexity Learned from a Reaction Corpus

(2018) Connor W. Coley et al.   Journal of Chemical Information and Modeling

De Novo Design of Bioactive Small Molecules by Artificial Intelligence

(2018) Daniel Merk et al.   Molecular Informatics

Points of Significance: Statistics versus machine learning

(2018) Danilo Bzdok et al.   NATURE METHODS

Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening

(2018) Rafaela Gladysz 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

Computational systems pharmacology analysis of cannabidiol: a combination of chemogenomics-knowledgebase network analysis and integrated in silico modeling and simulation

(2018) Yue-min Bian et al.   ACTA PHARMACOLOGICA SINICA

Five Years of the KNIME Vernalis Cheminformatics Community Contribution

(2018) Stephen Roughley   CURRENT MEDICINAL CHEMISTRY

Entangled Conditional Adversarial Autoencoder for de Novo Drug Discovery

(2018) Daniil Polykovskiy et al.   MOLECULAR PHARMACEUTICS

Planning chemical syntheses with deep neural networks and symbolic AI

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

Inverse molecular design using machine learning: Generative models for matter engineering

(2018) Benjamin Sanchez-Lengeling et al.   SCIENCE

Hunting for Organic Molecules with Artificial Intelligence: Molecules Optimized for Desired Excitation Energies

(2018) Masato Sumita et al.   ACS Central Science

Deep reinforcement learning for de novo drug design

(2018) Mariya Popova et al.   Science Advances

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations

(2017) Marcus Wieder 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

druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico

(2017) Artur Kadurin et al.   MOLECULAR PHARMACEUTICS

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

(2017) Egon L. Willighagen et al.   Journal of Cheminformatics

Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks

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

Rule of five in 2015 and beyond: Target and ligand structural limitations, ligand chemistry structure and drug discovery project decisions

(2016) Christopher A. Lipinski   ADVANCED DRUG DELIVERY REVIEWS

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

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

Recent Advances in Scaffold Hopping

(2016) Ye Hu et al.   JOURNAL OF MEDICINAL CHEMISTRY

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

Thalidomide-induced teratogenesis: History and mechanisms

(2015) Neil Vargesson   BIRTH DEFECTS RESEARCH PART C-EMBRYO TODAY-REVIEWS

An overview of molecular fingerprint similarity search in virtual screening

(2015) Ingo Muegge et al.   Expert Opinion on Drug Discovery

ZINC 15 – Ligand Discovery for Everyone

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

Deep learning

(2015) Yann LeCun et al.   NATURE

SureChEMBL: a large-scale, chemically annotated patent document database

(2015) George Papadatos et al.   NUCLEIC ACIDS RESEARCH

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

InChI, the IUPAC International Chemical Identifier

(2015) Stephen R Heller et al.   Journal of Cheminformatics

KNIME-CDK: Workflow-driven cheminformatics

(2013) Stephan Beisken et al.   BMC BIOINFORMATICS

Estimation of the size of drug-like chemical space based on GDB-17 data

(2013) P. G. Polishchuk et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

ASD v2.0: updated content and novel features focusing on allosteric regulation

(2013) Zhimin Huang et al.   NUCLEIC ACIDS RESEARCH

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

(2012) Lars Ruddigkeit et al.   Journal of Chemical Information and Modeling

Scientific workflow systems: Pipeline Pilot and KNIME

(2012) Wendy A. Warr   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI

(2012) Noel M O’Boyle   Journal of Cheminformatics

KNIME Workflow to Assess PAINS Filters in SMARTS Format. Comparison of RDKit and Indigo Cheminformatics Libraries

(2011) Simon Saubern et al.   Molecular Informatics

Open Babel: An open chemical toolbox

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

3D-QSAR in Drug Design - A Review

(2010) Jitender Verma et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Pharmacophore modeling and applications in drug discovery: challenges and recent advances

(2010) Sheng-Yong Yang   DRUG DISCOVERY TODAY

Extended-Connectivity Fingerprints

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

Comparative Analysis of Machine Learning Methods in Ligand-Based Virtual Screening of Large Compound Libraries

(2009) Xiao Ma et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

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

Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions

(2009) Peter Ertl et al.   Journal of Cheminformatics