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DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations

Chemical science (Cambridge), 2020-03, Vol.11 (9), p.2531-2557

2020

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Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

Briefings in bioinformatics, 2019-09, Vol.20 (5), p.1878-1912

2019

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Mutual annotation‐based prediction of protein domain functions with Domain2GO

Protein science, 2024-06, Vol.33 (6), p.e4988-n/a

2024

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Tools and data services registry: a community effort to document bioinformatics resources

Nucleic acids research, 2016-01, Vol.44 (D1), p.D38-D47

2016

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HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences

PeerJ (San Francisco, CA), 2018-08, Vol.6, p.e5298-e5298, Article e5298

Dogan, Tunca

2018

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ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature

BMC bioinformatics, 2018-09, Vol.19 (1), p.334-334, Article 334

2018

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DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks

Scientific reports, 2019-05, Vol.9 (1), p.7344, Article 7344

2019

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Machine learning-based prediction of drug approvals using molecular, physicochemical, clinical trial, and patent-related features

Expert opinion on drug discovery, 2022-12, Vol.17 (12), p.1425-1441

2022

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Learning functional properties of proteins with language models

Nature machine intelligence, 2022-03, Vol.4 (3), p.227-245

2022

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Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009171

2021

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CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

Nucleic acids research, 2021-09, Vol.49 (16), p.e96-e96

2021

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ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations

Computational and structural biotechnology journal, 2023-01, Vol.21, p.4743-4758

2023

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Transfer learning for drug–target interaction prediction

Bioinformatics (Oxford, England), 2023-06, Vol.39 (Supplement_1), p.i103-i110

2023

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SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins

Bioinformatics, 2022-09, Vol.38 (17), p.4226-4229

2022

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How to approach machine learning-based prediction of drug/compound–target interactions

Journal of cheminformatics, 2023-02, Vol.15 (1), p.16-16, Article 16

2023

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An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data

Computers in biology and medicine, 2024-02, Vol.169, p.107810-107810, Article 107810

2024

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UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

Bioinformatics (Oxford, England), 2016-08, Vol.32 (15), p.2264-2271

2016

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iBioProVis: interactive visualization and analysis of compound bioactivity space

Bioinformatics, 2020-08, Vol.36 (14), p.4227-4230

2020

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iBioProVis: interactive visualization and analysis of compound bioactivity space

Bioinformatics, 2020-11, Vol.36 (17), p.4674-4674

2020

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FAIR adoption, assessment and challenges at UniProt

Scientific data, 2019-09, Vol.6 (1), p.175-4, Article 175

2019

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ProFAB—open protein functional annotation benchmark

Briefings in bioinformatics, 2023-03, Vol.24 (2)

2023

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SELFormer: molecular representation learning via SELFIES language models

Machine learning: science and technology, 2023-06, Vol.4 (2), p.25035

2023

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A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules

Current topics in medicinal chemistry, 2018-01, Vol.18 (8), p.700-713

2018

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Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites

Methods in molecular biology (Clifton, N.J.), 2018-01, Vol.1762, p.51

2018

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Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences

PloS one, 2013-09, Vol.8 (9), p.e75458-e75458

2013

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DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

Mutual annotation‐based prediction of protein domain functions with Domain2GO

Tools and data services registry: a community effort to document bioinformatics resources

HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature

DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks

Machine learning-based prediction of drug approvals using molecular, physicochemical, clinical trial, and patent-related features

Learning functional properties of proteins with language models

Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases

CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations

Transfer learning for drug–target interaction prediction

SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins

How to approach machine learning-based prediction of drug/compound–target interactions

An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data

UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

iBioProVis: interactive visualization and analysis of compound bioactivity space

iBioProVis: interactive visualization and analysis of compound bioactivity space

FAIR adoption, assessment and challenges at UniProt

ProFAB—open protein functional annotation benchmark

SELFormer: molecular representation learning via SELFIES language models

A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules

Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites

Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences

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