The Experimentalist’s Guide to Machine Learning for Small Molecule Design

Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization

(2023) Matthew C. Chan et al.   Journal of Physical Chemistry B

Merging Data Curation and Machine Learning to Improve Nanomedicines

(2022) Chen Chen et al.   ADVANCED DRUG DELIVERY REVIEWS

Predicting the Activities of Drug Excipients on Biological Targets using One-Shot Learning

(2022) Xuenan Mi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Machine learning approaches to optimize small-molecule inhibitors for RNA targeting

(2022) Hadar Grimberg et al.   Journal of Cheminformatics

Recent Advances in Machine Learning Variant Effect Prediction Tools for Protein Engineering

(2022) Jesse Horne et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Hierarchical Clustering and Target-Independent QSAR for Antileishmanial Oxazole and Oxadiazole Derivatives

(2022) Henrique R. Teles et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Rickettsia Aglow: A Fluorescence Assay and Machine Learning Model to Identify Inhibitors of Intracellular Infection

(2022) Alexander Lemenze et al.   ACS Infectious Diseases

TAIGET: A small-molecule target identification and annotation web server

(2022) Xuxu Wei et al.   Frontiers in Pharmacology

GC/MS Profiling, In Vitro and In Silico Pharmacological Screening and Principal Component Analysis of Essential Oils from Three Exotic and Two Endemic Plants from Mauritius

(2021) Bibi Sharmeen Jugreet et al.   CHEMISTRY & BIODIVERSITY

Screening for gene expression fluctuations reveals latency-promoting agents of HIV

(2021) Yiyang Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromones: Privileged scaffold in anticancer drug discovery

(2021) Vaishali M. Patil et al.   Chemical Biology & Drug Design

Development and validation of consensus machine learning-based models for the prediction of novel small molecules as potential anti-tubercular agents

(2021) Mushtaq Ahmad Wani et al.   MOLECULAR DIVERSITY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Random forest classification for predicting lifespan-extending chemical compounds

(2021) Sofia Kapsiani et al.   Scientific Reports

Featurization strategies for protein–ligand interactions and their applications in scoring function development

(2021) Guoli Xiong et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

A machine learning regression model for the screening and design of potential SARS-CoV-2 protease inhibitors

(2021) Gabriela Ilona B. Janairo et al.   Network Modeling and Analysis in Health Informatics and Bioinformatics

Design, synthesis and screening of a drug discovery library based on an Eremophila-derived serrulatane scaffold

(2021) Chen Zhang et al.   PHYTOCHEMISTRY

A comprehensive survey on regularization strategies in machine learning

(2021) Yingjie Tian et al.   Information Fusion

Exploring sodium glucose cotransporter (SGLT2) inhibitors with machine learning approach: A novel hope in anti-diabetes drug discovery

(2021) Md Moinul et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Discovery of Small-Molecule Activators for Glucose-6-Phosphate Dehydrogenase (G6PD) Using Machine Learning Approaches

(2020) Madhu Sudhana Saddala et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Algorithmic discovery of dynamic models from infectious disease data

(2020) Jonathan Horrocks et al.   Scientific Reports

A semi-supervised learning framework for quantitative structure-activity regression modelling

(2020) Oliver Watson et al.   BIOINFORMATICS

Protein kinase inhibitors’ classification using K-Nearest neighbor algorithm

(2020) Roya Arian et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

A comparative analysis of gradient boosting algorithms

(2020) Candice Bentéjac et al.   ARTIFICIAL INTELLIGENCE REVIEW

Evaluation of Sampling and Cross-Validation Tuning Strategies for Regional-Scale Machine Learning Classification

(2019) Christopher A. Ramezan et al.   Remote Sensing

Investigating the impact of data normalization on classification performance

(2019) Dalwinder Singh et al.   APPLIED SOFT COMPUTING

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

SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules

(2019) Antoine Daina et al.   NUCLEIC ACIDS RESEARCH

Deep neural network concepts for background subtraction:A systematic review and comparative evaluation

(2019) Thierry Bouwmans et al.   NEURAL NETWORKS

Naïve Bayesian Models for Vero Cell Cytotoxicity

(2018) Alexander L. Perryman et al.   PHARMACEUTICAL RESEARCH

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

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

Clinically applicable deep learning for diagnosis and referral in retinal disease

(2018) Jeffrey De Fauw et al.   NATURE MEDICINE

Inferring single-trial neural population dynamics using sequential auto-encoders

(2018) Chethan Pandarinath et al.   NATURE METHODS

Deep reinforcement learning for de novo drug design

(2018) Mariya Popova et al.   Science Advances

High-throughput screening in colorectal cancer tissue-originated spheroids

(2018) Jumpei Kondo et al.   CANCER SCIENCE

A review of the Expectation Maximization algorithm in data-driven process identification

(2018) Nima Sammaknejad et al.   JOURNAL OF PROCESS CONTROL

Machine learning on sequential data using a recurrent weighted average

(2018) Jared Ostmeyer et al.   NEUROCOMPUTING

Model-free inference of direct network interactions from nonlinear collective dynamics

(2017) Jose Casadiego et al.   Nature Communications

Rama: a machine learning approach for ribosomal protein prediction in plants

(2017) Thales Francisco Mota Carvalho et al.   Scientific Reports

High-throughput identification and rational design of synergistic small-molecule pairs for combating and bypassing antibiotic resistance

(2017) Morgan A. Wambaugh et al.   PLOS BIOLOGY

In silico prediction of drug-target interaction networks based on drug chemical structure and protein sequences

(2017) Zhengwei Li et al.   Scientific Reports

Robust linear regression: A review and comparison

(2016) Chun Yu et al.   COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION

Minipigs as models in drug discovery

(2016) Vijay K. Singh et al.   Expert Opinion on Drug Discovery

Prediction of hERG Liability - Using SVM Classification, Bootstrapping and Jackknifing

(2016) Hongmao Sun et al.   Molecular Informatics

Metabolomics-Based Discovery of Small Molecule Biomarkers in Serum Associated with Dengue Virus Infections and Disease Outcomes

(2016) Natalia V. Voge et al.   PLoS Neglected Tropical Diseases

Cyclopentitol as a scaffold for a natural product-like compound library for drug discovery

(2015) Jalindar D. Padwal et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Chemometrics tools in QSAR/QSPR studies: A historical perspective

(2015) Saeed Yousefinejad et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Machine-learning approaches in drug discovery: methods and applications

(2015) Antonio Lavecchia   DRUG DISCOVERY TODAY

Machine learning: Trends, perspectives, and prospects

(2015) M. I. Jordan et al.   SCIENCE

SwissTargetPrediction: a web server for target prediction of bioactive small molecules

(2014) David Gfeller et al.   NUCLEIC ACIDS RESEARCH

A high-sensitivity ultra-high performance liquid chromatography/high-resolution time-of-flight mass spectrometry (UHPLC-HR-TOFMS) method for screening synthetic cannabinoids and other drugs of abuse in urine

(2013) Mira Sundström et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Applications of Machine Learning in Genomics and Systems Biology

(2013) Chunmei Liu et al.   Computational and Mathematical Methods in Medicine

Target identification and mechanism of action in chemical biology and drug discovery

(2013) Monica Schenone et al.   Nature Chemical Biology

Harvesting Classification Trees for Drug Discovery

(2012) Yan Yuan et al.   Journal of Chemical Information and Modeling

A review on empirical mode decomposition in fault diagnosis of rotating machinery

(2012) Yaguo Lei et al.   MECHANICAL SYSTEMS AND SIGNAL PROCESSING

Classification of microarrays; synergistic effects between normalization, gene selection and machine learning

(2011) Jenny Önskog et al.   BMC BIOINFORMATICS

Avoiding Pitfalls in Applying Prediction Models, As Illustrated by the Example of Prostate Cancer Diagnosis

(2011) H. Cammann et al.   CLINICAL CHEMISTRY

Innovative high-performance liquid chromatography method development for the screening of 19 antimalarial drugs based on a generic approach, using design of experiments, independent component analysis and design space

(2011) B. Debrus et al.   JOURNAL OF CHROMATOGRAPHY A

Design and Synthesis of Small Molecule RhoA Inhibitors: A New Promising Therapy for Cardiovascular Diseases?

(2011) Jing Deng et al.   JOURNAL OF MEDICINAL CHEMISTRY

Multigate transistors as the future of classical metal–oxide–semiconductor field-effect transistors

(2011) Isabelle Ferain et al.   NATURE

Nanometre-scale electronics with III–V compound semiconductors

(2011) Jesús A. del Alamo   NATURE

Algorithms for hierarchical clustering: an overview

(2011) Fionn Murtagh et al.   Wiley Interdisciplinary Reviews-Data Mining and Knowledge Discovery

Overcoming Variations in Nanometer-Scale Technologies

(2011) Sachin S. Sapatnekar   IEEE Journal on Emerging and Selected Topics in Circuits and Systems

Trends in Risks Associated With New Drug Development: Success Rates for Investigational Drugs

(2010) J A DiMasi et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Privileged scaffolds for library design and drug discovery

(2010) Matthew E Welsch et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Zebrafish: A Complete Animal Model for In Vivo Drug Discovery and Development

(2009) Chiranjib Chakraborty et al.   CURRENT DRUG METABOLISM

Empirical Orthogonal Functions: The Medium is the Message

(2009) Adam H. Monahan et al.   JOURNAL OF CLIMATE

Kernel methods in machine learning

(2008) Thomas Hofmann et al.   ANNALS OF STATISTICS

Machine Learning for In Silico Virtual Screening and Chemical Genomics: New Strategies

(2008) Jean-Philippe Vert et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

The lipopolysaccharide Parkinson’s disease animal model: mechanistic studies and drug discovery

(2008) Garima Dutta et al.   FUNDAMENTAL & CLINICAL PHARMACOLOGY

What is the expectation maximization algorithm?

(2008) Chuong B Do et al.   NATURE BIOTECHNOLOGY

Application of reinforcement learning for segmentation of transrectal ultrasound images

(2008) Farhang Sahba et al.   BMC MEDICAL IMAGING