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

DeepSurf: A surface-based deep learning approach for the prediction of ligand binding sites on proteins

(2021) Stelios K Mylonas et al.   BIOINFORMATICS

A Review on Compound-Protein Interaction Prediction Methods: Data, Format, Representation and Model

(2021) Sangsoo Lim et al.   Computational and Structural Biotechnology Journal

An effective self-supervised framework for learning expressive molecular global representations to drug discovery

(2021) Pengyong Li et al.   BRIEFINGS IN BIOINFORMATICS

Deep drug-target binding affinity prediction with multiple attention blocks

(2021) Yuni Zeng et al.   BRIEFINGS IN BIOINFORMATICS

Utilizing graph machine learning within drug discovery and development

(2021) Thomas Gaudelet et al.   BRIEFINGS IN BIOINFORMATICS

MultiDTI: drug–target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network

(2021) Deshan Zhou et al.   BIOINFORMATICS

Predicting potential small molecule–miRNA associations based on bounded nuclear norm regularization

(2021) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

Current status and future prospects of drug–target interaction prediction

(2021) Xiaoqing Ru et al.   Briefings in Functional Genomics

Progress in Research on Artificial Intelligence Applied to Polymorphism and Cocrystal Prediction

(2021) Tianyu Heng et al.   ACS Omega

Representation of molecules for drug response prediction

(2021) Xin An et al.   BRIEFINGS IN BIOINFORMATICS

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

GANsDTA: Predicting Drug-Target Binding Affinity Using GANs

(2020) Lingling Zhao et al.   Frontiers in Genetics

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

DeepCDA: Deep Cross-Domain Compound-Protein Affinity Prediction through LSTM and Convolutional Neural Networks

(2020) Karim Abbasi et al.   BIOINFORMATICS

Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

(2020) Natesh Singh et al.   BRIEFINGS IN BIOINFORMATICS

Machine learning models for drug–target interactions: current knowledge and future directions

(2020) Sofia D’Souza et al.   DRUG DISCOVERY TODAY

Similarity-Based Methods and Machine Learning Approaches for Target Prediction in Early Drug Discovery: Performance and Scope

(2020) Neann Mathai et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds

(2020) Jinsol Yang et al.   Journal of Chemical Information and Modeling

Improvement in ADMET Prediction with Multitask Deep Featurization

(2020) Evan N. Feinberg et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2020) Shuya Li et al.   Cell Systems

Bayer’s in silico ADMET platform: a journey of machine learning over the past two decades

(2020) Andreas H. Göller et al.   DRUG DISCOVERY TODAY

MDeePred: Novel Multi-Channel protein featurization for deep learning based binding affinity prediction in drug discovery

(2020) A S Rifaioglu et al.   BIOINFORMATICS

MolTrans: Molecular interaction transformer for drug target interaction prediction

(2020) Kexin Huang et al.   BIOINFORMATICS

Automated design and optimization of multitarget schizophrenia drug candidates by deep learning

(2020) Xiaoqin Tan et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Transfer learning enables the molecular transformer to predict regio- and stereoselective reactions on carbohydrates

(2020) Giorgio Pesciullesi et al.   Nature Communications

DeepPurpose: a deep learning library for drug–target interaction prediction

(2020) Kexin Huang et al.   BIOINFORMATICS

Deep learning enables discovery of highly potent anti-osteoporosis natural products

(2020) Zhihong Liu et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

ASRNN: A recurrent neural network with an attention model for sequence labeling

(2020) Jerry Chun-Wei Lin et al.   KNOWLEDGE-BASED SYSTEMS

An Overview of Scoring Functions Used for Protein–Ligand Interactions in Molecular Docking

(2019) Jin Li et al.   Interdisciplinary Sciences-Computational Life Sciences

Computational Model Development of Drug-Target Interaction Prediction: A Review

(2019) Qi Zhao et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

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

(2019) Mostafa Karimi et al.   BIOINFORMATICS

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing

(2019) Richard D. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

Applications of machine learning in drug discovery and development

(2019) Jessica Vamathevan et al.   NATURE REVIEWS DRUG DISCOVERY

Protein contact prediction using metagenome sequence data and residual neural networks

(2019) Qi Wu et al.   BIOINFORMATICS

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

(2019) Ingoo Lee et al.   PLoS Computational Biology

Computer vision algorithms and hardware implementations: A survey

(2019) Xin Feng et al.   INTEGRATION-THE VLSI JOURNAL

Predicting Drug–Target Interaction Using a Novel Graph Neural Network with 3D Structure-Embedded Graph Representation

(2019) Jaechang Lim et al.   Journal of Chemical Information and Modeling

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

(2019) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

OnionNet: a Multiple-Layer Intermolecular-Contact-Based Convolutional Neural Network for Protein–Ligand Binding Affinity Prediction

(2019) Liangzhen Zheng et al.   ACS Omega

A drug-likeness toolbox facilitates ADMET study in drug discovery

(2019) Chen-Yang Jia et al.   DRUG DISCOVERY TODAY

Graph Convolutional Neural Networks for Predicting Drug-Target Interactions

(2019) Wen Torng et al.   Journal of Chemical Information and Modeling

SNMFSMMA: using symmetric nonnegative matrix factorization and Kronecker regularized least squares to predict potential small molecule-microRNA association

(2019) Yan Zhao et al.   RNA Biology

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

(2019) Maryam Bagherian et al.   BRIEFINGS IN BIOINFORMATICS

To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map

(2019) Sheng Chen et al.   Journal of Chemical Information and Modeling

Gated CNN: Integrating multi-scale feature layers for object detection

(2019) Jin Yuan et al.   PATTERN RECOGNITION

Development and evaluation of a deep learning model for protein–ligand binding affinity prediction

(2018) Marta M Stepniewska-Dziubinska et al.   BIOINFORMATICS

Compound-protein Interaction Prediction with End-to-end Learning of Neural Networks for Graphs and Sequences

(2018) Masashi Tsubaki et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Open-source chemogenomic data-driven algorithms for predicting drug–target interactions

(2018) Ming Hao et al.   BRIEFINGS IN BIOINFORMATICS

Computational prediction of drug–target interactions using chemogenomic approaches: an empirical survey

(2018) Ali Ezzat et al.   BRIEFINGS IN BIOINFORMATICS

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

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

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

MoleculeNet: a benchmark for molecular machine learning

(2018) Zhenqin Wu et al.   Chemical Science

Development of a Protein-Ligand Extended Connectivity (PLEC) fingerprint and its application for binding affinity predictions

(2018) Maciej Wójcikowski et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

PconsC4: fast, accurate and hassle-free contact predictions

(2018) Mirco Michel et al.   BIOINFORMATICS

Deep learning and virtual drug screening

(2018) Kristy A Carpenter et al.   Future Medicinal Chemistry

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

(2018) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

Deep-Learning-Based Drug–Target Interaction Prediction

(2017) Ming Wen et al.   JOURNAL OF PROTEOME RESEARCH

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

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

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

(2017) Zixuan Cang et al.   PLoS Computational Biology

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

(2017) Sheng Wang et al.   PLoS Computational Biology

Interaction prediction in structure-based virtual screening using deep learning

(2017) Adam Gonczarek et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Boosting compound-protein interaction prediction by deep learning

(2016) Kai Tian et al.   METHODS

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Improving compound–protein interaction prediction by building up highly credible negative samples

(2015) Hui Liu et al.   BIOINFORMATICS

Drug–target interaction prediction: databases, web servers and computational models

(2015) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

Molecular fingerprint similarity search in virtual screening

(2015) Adrià Cereto-Massagué et al.   METHODS

Deep learning

(2015) Yann LeCun et al.   NATURE

The $2.6 Billion Pill — Methodologic and Policy Considerations

(2015) Jerry Avorn   NEW ENGLAND JOURNAL OF MEDICINE

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

(2015) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

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

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

InChI, the IUPAC International Chemical Identifier

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

From Feedforward to Recurrent LSTM Neural Networks for Language Modeling

(2015) Martin Sundermeyer et al.   IEEE-ACM Transactions on Audio Speech and Language Processing

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions

(2014) D.-S. Cao et al.   BIOINFORMATICS

Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis

(2014) Jing Tang et al.   Journal of Chemical Information and Modeling

Structural Protein–Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study

(2014) C. Da et al.   Journal of Chemical Information and Modeling

Effective Moment Feature Vectors for Protein Domain Structures

(2014) Jian-Yu Shi et al.   PLoS One

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules

(2013) Julian Schwartz et al.   Journal of Chemical Information and Modeling

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

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

Prediction of chemical–protein interactions: multitarget-QSAR versus computational chemogenomic methods

(2012) Feixiong Cheng et al.   Molecular BioSystems

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Structural Protein Descriptors in 1-Dimension and their Sequence-Based Predictions

(2011) Lukasz Kurgan et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Comprehensive analysis of kinase inhibitor selectivity

(2011) Mindy I Davis et al.   NATURE BIOTECHNOLOGY

Impact of high-throughput screening in biomedical research

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

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

(2011) H. B. Rao et al.   NUCLEIC ACIDS RESEARCH

Extended-Connectivity Fingerprints

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

How to improve R&D productivity: the pharmaceutical industry's grand challenge

(2010) Steven M. Paul et al.   NATURE REVIEWS DRUG DISCOVERY

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

ST-scale as a novel amino acid descriptor and its application in QSAM of peptides and analogues

(2009) Li Yang et al.   AMINO ACIDS

Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry

(2009) Donald S. Berkholz et al.   NUCLEIC ACIDS RESEARCH

IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding

(2009) R. Z. Cer et al.   NUCLEIC ACIDS RESEARCH