Computational approaches streamlining drug discovery

Modeling the expansion of virtual screening libraries

(2023) Jiankun Lyu et al.   Nature Chemical Biology

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

(2023) Stefan Gahbauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor

(2023) Feng Ren et al.   Chemical Science

Integrating structure-based approaches in generative molecular design

(2023) Morgan Thomas et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

(2023) Yuqi Zhang et al.   Journal of Chemical Information and Modeling

Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs

(2022) Louis Bellmann et al.   Journal of Chemical Information and Modeling

Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

(2022) Andreas Luttens et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Automated iterative Csp3-C bond formation

(2022) Daniel J. Blair et al.   NATURE

Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking

(2022) Francesco Gentile et al.   Nature Protocols

AI in small-molecule drug discovery: a coming wave?

(2022) Madura K.P. Jayatunga et al.   NATURE REVIEWS DRUG DISCOVERY

Non-covalent SARS-CoV-2 Mpro inhibitors developed from in silico screen hits

(2022) Giacomo G. Rossetti et al.   Scientific Reports

Why 90% of clinical drug development fails and how to improve it?

(2022) Duxin Sun et al.   Acta Pharmaceutica Sinica B

Digitizing Chemical Synthesis in 3D Printed Reactionware

(2022) Andrius Bubliauskas et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Exploration of Ultralarge Compound Collections for Drug Discovery

(2022) Wendy A. Warr et al.   Journal of Chemical Information and Modeling

Special Issue on Reaction Informatics and Chemical Space

(2022) Matthias Rarey et al.   Journal of Chemical Information and Modeling

On the Frustration to Predict Binding Affinities from Protein–Ligand Structures with Deep Neural Networks

(2022) Mikhail Volkov et al.   JOURNAL OF MEDICINAL CHEMISTRY

Defining Levels of Automated Chemical Design

(2022) Brian Goldman et al.   JOURNAL OF MEDICINAL CHEMISTRY

Machine Learning May Sometimes Simply Capture Literature Popularity Trends: A Case Study of Heterocyclic Suzuki–Miyaura Coupling

(2022) Wiktor Beker et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ni-electrocatalytic Csp3–Csp3 doubly decarboxylative coupling

(2022) Benxiang Zhang et al.   NATURE

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

(2022) Suzanne Ackloo et al.   Nature Reviews Chemistry

AlphaFold2 versus experimental structures: evaluation on G protein-coupled receptors

(2022) Xin-heng He et al.   ACTA PHARMACOLOGICA SINICA

Benchmarking AlphaFold ‐enabled molecular docking predictions for antibiotic discovery

(2022) Felix Wong et al.   Molecular Systems Biology

Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity

(2022) Anat Levit Kaplan et al.   NATURE

Chemical space docking enables large-scale structure-based virtual screening to discover ROCK1 kinase inhibitors

(2022) Paul Beroza et al.   Nature Communications

AlphaFill: enriching AlphaFold models with ligands and cofactors

(2022) Maarten L. Hekkelman et al.   NATURE METHODS

A structural biology community assessment of AlphaFold2 applications

(2022) Mehmet Akdel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries

(2021) Miljan Kuljanin et al.   NATURE BIOTECHNOLOGY

A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening

(2021) Christoph Gorgulla et al.   iScience

Utilizing graph machine learning within drug discovery and development

(2021) Thomas Gaudelet et al.   BRIEFINGS IN BIOINFORMATICS

Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference

(2021) Derek Jones et al.   Journal of Chemical Information and Modeling

Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein–Ligand Binding

(2021) Edward B. Miller et al.   Journal of Chemical Theory and Computation

Development of a graph convolutional neural network model for efficient prediction of protein-ligand binding affinities

(2021) Jeongtae Son et al.   PLoS One

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

(2021) Marion Schuller et al.   Science Advances

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Crowdsourced mapping of unexplored target space of kinase inhibitors

(2021) Anna Cichońska et al.   Nature Communications

Combining generative artificial intelligence and on-chip synthesis for de novo drug design

(2021) Francesca Grisoni et al.   Science Advances

From computer-aided drug discovery to computer-driven drug discovery

(2021) Leah Frye et al.   Drug Discovery Today: Technologies

Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review

(2021) Victor T. Sabe et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry

(2021) Yuliana Zabolotna et al.   Journal of Chemical Information and Modeling

Efficient Exploration of Chemical Space with Docking and Deep Learning

(2021) Ying Yang et al.   Journal of Chemical Theory and Computation

Synthon-based ligand discovery in virtual libraries of over 11 billion compounds

(2021) Arman A. Sadybekov et al.   NATURE

Structures of the σ2 receptor enable docking for bioactive ligand discovery

(2021) Assaf Alon et al.   NATURE

A practical guide to large-scale docking

(2021) Brian J. Bender et al.   Nature Protocols

Structure-Based Virtual Screening for Ligands of G Protein–Coupled Receptors: What Can Molecular Docking Do for You?

(2021) Flavio Ballante et al.   PHARMACOLOGICAL REVIEWS

Applying and improving AlphaFold at CASP14

(2021) John Jumper et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19

(2021) Dafydd R. Owen et al.   SCIENCE

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2020) Conor D. Parks et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

(2020) Reed M. Stein et al.   NATURE

Veridical data science

(2020) Bin Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next generation 3D pharmacophore modeling

(2020) David Schaller et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery

(2020) Lauro Ribeiro de Souza Neto et al.   Frontiers in Chemistry

Impact of GPCR Structures on Drug Discovery

(2020) Miles Congreve et al.   CELL

Rapid Identification of Potential Inhibitors of SARS‐CoV‐2 Main Protease by Deep Docking of 1.3 Billion Compounds

(2020) Anh-Tien Ton et al.   Molecular Informatics

An open-source drug discovery platform enables ultra-large virtual screens

(2020) Christoph Gorgulla et al.   NATURE

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

(2020) Zhenming Jin et al.   NATURE

Improving detection of protein-ligand binding sites with 3D segmentation

(2020) Marta M. Stepniewska-Dziubinska et al.   Scientific Reports

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

(2020) Vincent Blay et al.   DRUG DISCOVERY TODAY

Rigorous Free Energy Simulations in Virtual Screening

(2020) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Machine Learning on DNA-Encoded Libraries: A New Paradigm for Hit Finding

(2020) Kevin McCloskey et al.   JOURNAL OF MEDICINAL CHEMISTRY

Improving the Accuracy of Predicted Human Pharmacokinetics: Lessons Learned from the AstraZeneca Drug Pipeline Over Two Decades

(2020) Michael Davies et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

The Advent of Generative Chemistry

(2020) Quentin Vanhaelen et al.   ACS Medicinal Chemistry Letters

DNA-Encoded Chemistry: Drug Discovery from a Few Good Reactions

(2020) Patrick R. Fitzgerald et al.   CHEMICAL REVIEWS

Can easy chemistry produce complex, diverse, and novel molecules?

(2020) Anna Tomberg et al.   DRUG DISCOVERY TODAY

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects

(2020) Christina E. M. Schindler et al.   Journal of Chemical Information and Modeling

Generating multibillion chemical space of readily accessible screening compounds

(2020) Oleksandr O. Grygorenko et al.   iScience

Advanced machine-learning techniques in drug discovery

(2020) Moe Elbadawi 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

D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

(2019) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Ultra-large library docking for discovering new chemotypes

(2019) Jiankun Lyu et al.   NATURE

The next level in chemical space navigation: going far beyond enumerable compound libraries

(2019) Torsten Hoffmann et al.   DRUG DISCOVERY TODAY

The cryo-EM method microcrystal electron diffraction (MicroED)

(2019) Brent L. Nannenga et al.   NATURE METHODS

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

Prediction of Oral Bioavailability in Rats: Transferring Insights from in Vitro Correlations to (Deep) Machine Learning Models Using in Silico Model Outputs and Chemical Structure Parameters

(2019) Sebastian Schneckener et al.   Journal of Chemical Information and Modeling

Fragment-based drug discovery using cryo-EM

(2019) Michael Saur et al.   DRUG DISCOVERY TODAY

Rethinking drug design in the artificial intelligence era

(2019) Petra Schneider et al.   NATURE REVIEWS DRUG DISCOVERY

The Molecular Industrial Revolution: Automated Synthesis of Small Molecules

(2018) Melanie Trobe et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information

(2018) Dario Neri et al.   Annual Review of Biochemistry

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

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

Cryo-EM in drug discovery: achievements, limitations and prospects

(2018) Jean-Paul Renaud et al.   NATURE REVIEWS DRUG DISCOVERY

Virtual Chemical Libraries

(2018) W. Patrick Walters   JOURNAL OF MEDICINAL CHEMISTRY

Planning chemical syntheses with deep neural networks and symbolic AI

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

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

(2016) Jeffrey R. Wagner et al.   CHEMICAL REVIEWS

AutoQSAR: an automated machine learning tool for best-practice quantitative structure–activity relationship modeling

(2016) Steven L Dixon et al.   Future Medicinal Chemistry

The Proximal Lilly Collection: Mapping, Exploring and Exploiting Feasible Chemical Space

(2016) Christos A. Nicolaou et al.   Journal of Chemical Information and Modeling

Unravelling biological macromolecules with cryo-electron microscopy

(2016) Rafael Fernandez-Leiro et al.   NATURE

Structure-based discovery of opioid analgesics with reduced side effects

(2016) Aashish Manglik et al.   NATURE

A comprehensive map of molecular drug targets

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

Network-based in silico drug efficacy screening

(2016) Emre Guney et al.   Nature Communications

Role of computer-aided drug design in modern drug discovery

(2015) Stephani Joy Y. Macalino et al.   ARCHIVES OF PHARMACAL RESEARCH

FOCUS — Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists

(2015) Nikolaus Stiefl et al.   Journal of Chemical Information and Modeling

Synthesis of many different types of organic small molecules using one automated process

(2015) J. Li et al.   SCIENCE

SuFEx-Based Synthesis of Polysulfates

(2014) Jiajia Dong et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

Crystallography: Atomic secrets

(2014) Nicola Jones   NATURE

QSAR Modeling: Where Have You Been? Where Are You Going To?

(2013) Artem Cherkasov et al.   JOURNAL OF MEDICINAL CHEMISTRY

Serial Femtosecond Crystallography of G Protein-Coupled Receptors

(2013) W. Liu et al.   SCIENCE

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

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

Pfizer Global Virtual Library (PGVL): A Chemistry Design Tool Powered by Experimentally Validated Parallel Synthesis Information

(2012) Qiyue Hu et al.   ACS Combinatorial Science

A Collection of Robust Organic Synthesis Reactions forIn SilicoMolecule Design

(2011) Markus Hartenfeller et al.   Journal of Chemical Information and Modeling

Ligand discovery from a dopamine D3 receptor homology model and crystal structure

(2011) Jens Carlsson et al.   Nature Chemical Biology

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

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

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

Flexible ligand docking using conformational ensembles

(2010) David M. Lorber et al.   PROTEIN SCIENCE

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE