Artificial intelligence in drug design

Deep neural network in QSAR studies using deep belief network

(2018) Fahimeh Ghasemi et al.   APPLIED SOFT COMPUTING

SCScore: Synthetic Complexity Learned from a Reaction Corpus

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

Inner and Outer Recursive Neural Networks for Chemoinformatics Applications

(2018) Gregor Urban et al.   Journal of Chemical Information and Modeling

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

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

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

Machine-Learning-Assisted Approach for Discovering Novel Inhibitors Targeting Bromodomain-Containing Protein 4

(2017) Jing Xing et al.   Journal of Chemical Information and Modeling

Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction

(2017) Youjun Xu et al.   Journal of Chemical Information and Modeling

Is Multitask Deep Learning Practical for Pharma?

(2017) Bharath Ramsundar et al.   Journal of Chemical Information and Modeling

Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction

(2017) Connor W. Coley et al.   Journal of Chemical Information and Modeling

In silico structure-based approaches to discover protein-protein interaction-targeting drugs

(2017) Woong-Hee Shin et al.   METHODS

De novo Drug Design - Ye olde Scoring Problem Revisited

(2017) Gisbert Schneider et al.   Molecular Informatics

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

The drug-maker's guide to the galaxy

(2017) Asher Mullard   NATURE

The AI detectives

(2017) Paul Voosen   SCIENCE

The target landscape of clinical kinase drugs

(2017) Susan Klaeger et al.   SCIENCE

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

(2017) Yunan Luo et al.   Nature Communications

Molecular de-novo design through deep reinforcement learning

(2017) Marcus Olivecrona et al.   Journal of Cheminformatics

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

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

Computational methods in drug discovery

(2016) Sumudu P Leelananda et al.   Beilstein Journal of Organic Chemistry

A simple model predicts UGT-mediated metabolism

(2016) Na Le Dang et al.   BIOINFORMATICS

A Short Review of the Generation of Molecular Descriptors and Their Applications in Quantitative Structure Property/Activity Relationships

(2016) Sagarika Sahoo et al.   Current Computer-Aided Drug Design

Computer Aided Drug Design: Success and Limitations

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

Descriptors and their selection methods in QSAR analysis: paradigm for drug design

(2016) Danishuddin et al.   DRUG DISCOVERY TODAY

Boosting Docking-Based Virtual Screening with Deep Learning

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

Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches

(2016) Govindan Subramanian et al.   Journal of Chemical Information and Modeling

ADME Properties Evaluation in Drug Discovery: Prediction of Caco-2 Cell Permeability Using a Combination of NSGA-II and Boosting

(2016) Ning-Ning Wang et al.   Journal of Chemical Information and Modeling

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest

(2016) Cheng Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Template-based identification of protein–protein interfaces using e FindSite PPI

(2016) Surabhi Maheshwari et al.   METHODS

Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning

(2016) Tianchuan Du et al.   METHODS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Small molecules, big targets: drug discovery faces the protein–protein interaction challenge

(2016) Duncan E. Scott et al.   NATURE REVIEWS DRUG DISCOVERY

A comprehensive map of molecular drug targets

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

Elucidating the druggable interface of protein−protein interactions using fragment docking and coevolutionary analysis

(2016) Fang Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Artur Kadurin et al.   Oncotarget

Machine learning in computational docking

(2015) Mohamed A. Khamis et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Computational prediction of protein interfaces: A review of data driven methods

(2015) Li C. Xue et al.   FEBS LETTERS

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

(2015) Matt Spencer et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Deep Neural Nets as a Method for Quantitative Structure–Activity Relationships

(2015) Junshui Ma et al.   Journal of Chemical Information and Modeling

Design of chemical space networks on the basis of Tversky similarity

(2015) Mengjun Wu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Human-level control through deep reinforcement learning

(2015) Volodymyr Mnih et al.   NATURE

Deep learning

(2015) Yann LeCun et al.   NATURE

Inhibition of human copper trafficking by a small molecule significantly attenuates cancer cell proliferation

(2015) Jing Wang et al.   Nature Chemistry

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

iPPI-DB: an online database of modulators of protein–protein interactions

(2015) Céline M. Labbé et al.   NUCLEIC ACIDS RESEARCH

Beware of docking!

(2015) Yu-Chian Chen   TRENDS IN PHARMACOLOGICAL SCIENCES

Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field

(2015) Maciej Wójcikowski et al.   Journal of Cheminformatics

InChI, the IUPAC International Chemical Identifier

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

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

(2015) Qurrat Ul Ain et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

XenoSite server: a web-available site of metabolism prediction tool

(2014) M. K. Matlock et al.   BIOINFORMATICS

Drug repositioning by integrating target information through a heterogeneous network model

(2014) Wenhui Wang et al.   BIOINFORMATICS

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

In Silico Machine Learning Methods in Drug Development

(2014) Dimitar Dobchev et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Structure-based design of small-molecule protein–protein interaction modulators: the story so far

(2014) Federico Falchi et al.   Future Medicinal Chemistry

Clearance Mechanism Assignment and Total Clearance Prediction in Human Based upon in Silico Models

(2014) Franco Lombardo et al.   JOURNAL OF MEDICINAL CHEMISTRY

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Metformin promotes lifespan through mitohormesis via the peroxiredoxin PRDX-2

(2014) W. De Haes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hot spots in protein–protein interfaces: Towards drug discovery

(2014) Engin Cukuroglu et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

ChemoPy: freely available python package for computational biology and chemoinformatics

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

Metformin Retards Aging in C. elegans by Altering Microbial Folate and Methionine Metabolism

(2013) Filipe Cabreiro et al.   CELL

Virtual Screening Strategies in Drug Discovery: A Critical Review

(2013) A. Lavecchia et al.   CURRENT MEDICINAL CHEMISTRY

Protein–protein interactions as druggable targets: recent technological advances

(2013) Alicia P Higueruelo et al.   CURRENT OPINION IN PHARMACOLOGY

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules

(2013) Alessandro Lusci et al.   Journal of Chemical Information and Modeling

XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks

(2013) Jed Zaretzki et al.   Journal of Chemical Information and Modeling

Time-Split Cross-Validation as a Method for Estimating the Goodness of Prospective Prediction.

(2013) Robert P. Sheridan   Journal of Chemical Information and Modeling

Metformin improves healthspan and lifespan in mice

(2013) Alejandro Martin-Montalvo et al.   Nature Communications

Comparison of Random Forest and Pipeline Pilot Naïve Bayes in Prospective QSAR Predictions

(2012) Bin Chen et al.   Journal of Chemical Information and Modeling

ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions

(2012) Iurii Sushko 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

Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic

(2010) Tanaji Talele et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

In silico structure-activity-relationship (SAR) models from machine learning: a review

(2010) Xia Ning et al.   DRUG DEVELOPMENT RESEARCH

Mechanisms of Drug Toxicity and Relevance to Pharmaceutical Development

(2010) F. Peter Guengerich   Drug Metabolism and Pharmacokinetics

Pharmacophore-based virtual screening: a review of recent applications

(2010) Kyun-Hwan Kim et al.   Expert Opinion on Drug Discovery

The dynamics of drug-target interactions: drug-target residence time and its impact on efficacy and safety

(2010) Robert A Copeland   Expert Opinion on Drug Discovery

Recent Advances in Fragment-Based QSAR and Multi-Dimensional QSAR Methods

(2010) Kyaw Zeyar Myint et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

(2010) Sheng-You Huang et al.   Journal of Chemical Information and Modeling

Extended-Connectivity Fingerprints

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

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

(2010) Chun Wei Yap   JOURNAL OF COMPUTATIONAL CHEMISTRY

Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

(2010) Sheng-You Huang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Protein interface conservation across structure space

(2010) Q. C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Machine Learning in Virtual Screening

(2009) James Melville et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

A Survey on Transfer Learning

(2009) Sinno Jialin Pan et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

SVM Model for Virtual Screening of Lck Inhibitors

(2009) Chin Y. Liew et al.   Journal of Chemical Information and Modeling

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces

(2008) Y. Yamanishi et al.   BIOINFORMATICS

The effect of ultrasonic pre-treatment on the catalytic activity of lipases in aqueous and non-aqueous media

(2008) Shweta Shah et al.   Chemistry Central Journal