The Application of Artificial Intelligence Accelerates G Protein-Coupled Receptor Ligand Discovery

The application of artificial intelligence to accelerate G protein‐coupled receptor drug discovery

(2023) Anh T. N. Nguyen et al.   BRITISH JOURNAL OF PHARMACOLOGY

Structural basis of efficacy-driven ligand selectivity at GPCRs

(2023) Alexander S. Powers et al.   Nature Chemical Biology

Chemistry-intuitive explanation of graph neural networks for molecular property prediction with substructure masking

(2023) Zhenxing Wu et al.   Nature Communications

IPs-GRUAtt: An attention-based bidirectional gated recurrent unit network for predicting phosphorylation sites of SARS-CoV-2 infection

(2023) Guiyang Zhang et al.   Molecular Therapy-Nucleic Acids

Artificial intelligence for drug discovery: Resources, methods, and applications

(2023) Wei Chen et al.   Molecular Therapy-Nucleic Acids

Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors

(2022) Lorenzo Di Rienzo et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

GPCR systems pharmacology: a different perspective on the development of biased therapeutics

(2022) Dylan Scott Eiger et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

Critical roles of G protein-coupled receptors in regulating intestinal homeostasis and inflammatory bowel disease

(2022) Zhongsheng Feng et al.   Mucosal Immunology

Structure-Based Discovery of Negative Allosteric Modulators of the Metabotropic Glutamate Receptor 5

(2022) Stefanie Kampen et al.   ACS Chemical Biology

A machine learning model for classifying G-protein-coupled receptors as agonists or antagonists

(2022) Jooseong Oh et al.   BMC BIOINFORMATICS

PubChem 2023 update

(2022) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources

(2022) Gáspár Pándy-Szekeres et al.   NUCLEIC ACIDS RESEARCH

UniProt: the Universal Protein Knowledgebase in 2023

(2022) et al.   NUCLEIC ACIDS RESEARCH

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

(2022) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction

(2022) Sumin Lee et al.   Computational and Structural Biotechnology Journal

New machine learning and physics-based scoring functions for drug discovery

(2021) Isabella A. Guedes et al.   Scientific Reports

Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study

(2021) Morgan Thomas et al.   Journal of Cheminformatics

Integrated Multi-Class Classification and Prediction of GPCR Allosteric Modulators by Machine Learning Intelligence

(2021) Tianling Hou et al.   Biomolecules

Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the β1-adrenergic receptor

(2020) J. Niclas Frei et al.   Nature Communications

Advances in G protein-coupled receptor high-throughput screening

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

Virtual Screening of Human Class-A GPCRs Using Ligand Profiles Built on Multiple Ligand–Receptor Interactions

(2020) Wallace K.B. Chan et al.   JOURNAL OF MOLECULAR BIOLOGY

Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition

(2020) Sebastian Raschka et al.   METHODS

Anti-inflammatory signaling through G protein-coupled receptors

(2020) Yun-jun Ge et al.   ACTA PHARMACOLOGICA SINICA

Classifying the superfamily of small heat shock proteins by using g-gap dipeptide compositions

(2020) Pengmian Feng et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Automated discovery of GPCR bioactive ligands

(2019) Sebastian Raschka   CURRENT OPINION IN STRUCTURAL BIOLOGY

Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors

(2019) Jiansheng Wu et al.   BIOINFORMATICS

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

(2019) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

Physiological roles for neuromodulation via Gi/o GPCRs working through Gβγ–SNARE interaction

(2019) Heidi E. Hamm et al.   NEUROPSYCHOPHARMACOLOGY

Learning a functional grammar of protein domains using natural language word embedding techniques

(2019) Daniel W. A. Buchan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The nature of efficacy at G protein-coupled receptors

(2019) Peishen Zhao et al.   BIOCHEMICAL PHARMACOLOGY

Classification of adaptor proteins using recurrent neural networks and PSSM profiles

(2019) Nguyen Quoc Khanh Le et al.   BMC GENOMICS

WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest

(2018) Jiansheng Wu et al.   BIOINFORMATICS

GPCRs: Emerging anti-cancer drug targets

(2018) Ainhoa Nieto Gutierrez et al.   CELLULAR SIGNALLING

Prediction of GPCR-Ligand Binding Using Machine Learning Algorithms

(2018) Sangmin Seo et al.   Computational and Mathematical Methods in Medicine

G Protein-Coupled Receptors as Targets for Approved Drugs: How Many Targets and How Many Drugs?

(2018) Krishna Sriram et al.   MOLECULAR PHARMACOLOGY

Fingerprint-Based Machine Learning Approach to Identify Potent and Selective 5-HT2BR Ligands

(2018) Krzysztof Rataj et al.   MOLECULES

Targeting G protein-coupled receptor signalling by blocking G proteins

(2018) Adrian P. Campbell et al.   NATURE REVIEWS DRUG DISCOVERY

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

(2018) Benjamin Sanchez-Lengeling et al.   SCIENCE

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions

(2018) Thomas D Newport et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

Discovery of new GPCR ligands to illuminate new biology

(2017) Bryan L Roth et al.   Nature Chemical Biology

Trends in GPCR drug discovery: new agents, targets and indications

(2017) Alexander S. Hauser et al.   NATURE REVIEWS DRUG DISCOVERY

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

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

Molecular de-novo design through deep reinforcement learning

(2017) Marcus Olivecrona et al.   Journal of Cheminformatics

Scalable Algorithms for Multi-Instance Learning

(2017) Xiu-Shen Wei et al.   IEEE Transactions on Neural Networks and Learning Systems

Structure-based discovery of opioid analgesics with reduced side effects

(2016) Aashish Manglik et al.   NATURE

GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors

(2016) Mauricio Esguerra et al.   NUCLEIC ACIDS RESEARCH

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations

(2015) Wallace K. B. Chan et al.   BIOINFORMATICS

GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome

(2015) Jian Zhang et al.   STRUCTURE

Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model

(2014) Yang Cao et al.   BIOINFORMATICS

GOMoDo: A GPCRs Online Modeling and Docking Webserver

(2013) Massimo Sandal et al.   PLoS One

Orthosteric versus allosteric GPCR activation: The great challenge of group-III mGluRs

(2012) Peter J. Flor et al.   BIOCHEMICAL PHARMACOLOGY

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Signaling by Sensory Receptors

(2011) D. Julius et al.   Cold Spring Harbor Perspectives in Biology

GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation

(2010) Jian Zhang et al.   BIOINFORMATICS

Extended-Connectivity Fingerprints

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

Biophysical dissection of membrane proteins

(2009) Stephen H. White   NATURE

gpDB: a database of GPCRs, G-proteins, effectors and their interactions

(2008) Margarita C. Theodoropoulou et al.   BIOINFORMATICS

Structural diversity of G protein-coupled receptors and significance for drug discovery

(2008) Malin C. Lagerström et al.   NATURE REVIEWS DRUG DISCOVERY