Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 2: a discussion of chemical and biological data

Bayer’s in silico ADMET platform: a journey of machine learning over the past two decades

(2020) Andreas H. Göller et al.   DRUG DISCOVERY TODAY

Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 1: Ways to make an impact, and why we are not there yet

(2020) Andreas Bender et al.   DRUG DISCOVERY TODAY

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

(2020) Ewen Callaway   NATURE

Association of Combined Naltrexone and Ketamine With Depressive Symptoms in a Case series of Patients With Depression and Alcohol Use Disorder

(2019) Gihyun Yoon et al.   JAMA Psychiatry

Separating host and microbiome contributions to drug pharmacokinetics and toxicity

(2019) Michael Zimmermann et al.   SCIENCE

Curation and analysis of clinical pathology parameters and histopathologic findings from eTOXsys, a large database project (eTOX) for toxicologic studies

(2019) Mark D. Pinches et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

The mechanisms of pharmacokinetic food-drug interactions – A perspective from the UNGAP group

(2019) Mirko Koziolek et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

Analyzing Learned Molecular Representations for Property Prediction

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

KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images

(2019) Isidro Cortés-Ciriano et al.   Journal of Cheminformatics

A review of methods for solubility determination in biopharmaceutical drug characterization

(2019) Ardita Veseli et al.   DRUG DEVELOPMENT AND INDUSTRIAL PHARMACY

Attenuation of antidepressant and antisuicidal effects of ketamine by opioid receptor antagonism

(2019) Nolan R. Williams et al.   MOLECULAR PSYCHIATRY

Artificial intelligence in digital pathology — new tools for diagnosis and precision oncology

(2019) Kaustav Bera et al.   Nature Reviews Clinical Oncology

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

(2019) Philippe Schwaller et al.   ACS Central Science

Biased signalling: from simple switches to allosteric microprocessors

(2018) Jeffrey S. Smith et al.   NATURE REVIEWS DRUG DISCOVERY

In vitro to in vivo extrapolation for high throughput prioritization and decision making

(2018) Shannon M. Bell et al.   TOXICOLOGY IN VITRO

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

(2018) Haotian Teng et al.   GigaScience

Toxic Colors: The Use of Deep Learning for Predicting Toxicity of Compounds Merely from Their Graphic Images

(2018) Michael Fernandez et al.   Journal of Chemical Information and Modeling

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

The germline genetic component of drug sensitivity in cancer cell lines

(2018) Michael P. Menden et al.   Nature Communications

Open Targets Platform: new developments and updates two years on

(2018) Denise Carvalho-Silva et al.   NUCLEIC ACIDS RESEARCH

PotentialNet for Molecular Property Prediction

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

A look at ligand binding thermodynamics in drug discovery

(2017) Rafael Claveria-Gimeno et al.   Expert Opinion on Drug Discovery

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

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

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

Data Standardization, Pharmaceutical Drug Development, and the 3Rs

(2016) Laura Kaufman et al.   ILAR JOURNAL

NMDAR inhibition-independent antidepressant actions of ketamine metabolites

(2016) Panos Zanos et al.   NATURE

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

(2016) David Silver et al.   NATURE

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

(2016) Ruili Huang et al.   Nature Communications

When Quality Beats Quantity: Decision Theory, Drug Discovery, and the Reproducibility Crisis

(2016) Jack W. Scannell et al.   PLoS One

The role of ontologies in biological and biomedical research: a functional perspective

(2015) R. Hoehndorf et al.   BRIEFINGS IN BIOINFORMATICS

Snakes on a Plane: A perfect snap for bioimage analysis

(2015) Ricard Delgado-Gonzalo et al.   IEEE SIGNAL PROCESSING MAGAZINE

ZINC 15 – Ligand Discovery for Everyone

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

The SIDER database of drugs and side effects

(2015) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

Bias in Spontaneous Reporting of Adverse Drug Reactions in Japan

(2015) Shinichi Matsuda et al.   PLoS One

Open TG-GATEs: a large-scale toxicogenomics database

(2014) Yoshinobu Igarashi et al.   NUCLEIC ACIDS RESEARCH

Impact of Genetic Polymorphism on Drug-Drug Interactions Mediated by Cytochromes: A General Approach

(2013) Michel Tod et al.   AAPS Journal

Toward a new paradigm for the efficient in vitro–in vivo extrapolation of metabolic clearance in humans from hepatocyte data

(2013) Patrick Poulin et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods

(2010) Vishwesh Venkatraman et al.   Journal of Chemical Information and Modeling

Deep, Big, Simple Neural Nets for Handwritten Digit Recognition

(2010) Dan Claudiu Cireşan et al.   NEURAL COMPUTATION

Healthy skepticism: assessing realistic model performance

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

Sequences and consequences

(2009) S. Brenner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES