Pmf-cpi: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions

Predictive Models for Human Cytochrome P450 3A7 Selective Inhibitors and Substrates

(2023) Tuan Xu et al.   Journal of Chemical Information and Modeling

Evolutionary-scale prediction of atomic-level protein structure with a language model

(2023) Zeming Lin et al.   SCIENCE

Improving the generalizability of protein-ligand binding predictions with AI-Bind

(2023) Ayan Chatterjee et al.   Nature Communications

BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction

(2022) Min Li et al.   BIOINFORMATICS

Effective drug-target interaction prediction with mutual interaction neural network

(2022) Fei Li et al.   BIOINFORMATICS

Compound–protein interaction prediction by deep learning: Databases, descriptors and models

(2022) Bing-Xue Du et al.   DRUG DISCOVERY TODAY

Structure-Aware Multimodal Deep Learning for Drug–Protein Interaction Prediction

(2022) Penglei Wang et al.   Journal of Chemical Information and Modeling

ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding

(2022) Junjie Wang et al.   Journal of Cheminformatics

A multitask GNN-based interpretable model for discovery of selective JAK inhibitors

(2022) Yimeng Wang et al.   Journal of Cheminformatics

AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification

(2022) Mehdi Yazdani-Jahromi et al.   BRIEFINGS IN BIOINFORMATICS

CoaDTI: multi-modal co-attention based framework for drug–target interaction annotation

(2022) Lei Huang et al.   BRIEFINGS IN BIOINFORMATICS

DeepBLI: A Transferable Multichannel Model for Detecting β-Lactamase-Inhibitor Interaction

(2022) Ruihan Dong et al.   Journal of Chemical Information and Modeling

Target-specific compound selectivity for multi-target drug discovery and repurposing

(2022) Tianduanyi Wang et al.   Frontiers in Pharmacology

DrugAI: a multi-view deep learning model for predicting drug–target activating/inhibiting mechanisms

(2022) Siqin Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction

(2021) QHwan Kim et al.   BIOINFORMATICS

Current and future status of JAK inhibitors

(2021) Donal P McLornan et al.   LANCET

DeepFusionDTA: Drug-Target Binding Affinity Prediction With Information Fusion and Hybrid Deep-Learning Ensemble Model

(2021) Yuqian Pu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments

(2020) Lifan Chen et al.   BIOINFORMATICS

Quantitative prediction of selectivity between the A1 and A2A adenosine receptors

(2020) Lindsey Burggraaff et al.   Journal of Cheminformatics

MONN: A Multi-objective Neural Network for Predicting Compound-Protein Interactions and Affinities

(2020) Shuya Li et al.   Cell Systems

DeepAffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks

(2019) Mostafa Karimi et al.   BIOINFORMATICS

Deep Learning Enhancing Kinome-Wide Polypharmacology Profiling: Model Construction and Experiment Validation

(2019) Xutong Li et al.   JOURNAL OF MEDICINAL CHEMISTRY

A Selectivity Study of FFAR4/FFAR1 Agonists by Molecular Modeling

(2019) Xiangying Zhang et al.   Journal of Chemical Information and Modeling

Machine learning approaches and databases for prediction of drug–target interaction: a survey paper

(2019) Maryam Bagherian et al.   BRIEFINGS IN BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

Impact of high-throughput screening in biomedical research

(2011) Ricardo Macarron et al.   NATURE REVIEWS DRUG DISCOVERY