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

PLoS computational biology, 2017-01, Vol.13 (1), p.e1005324-e1005324

2017

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Propagating annotations of molecular networks using in silico fragmentation

PLoS computational biology, 2018-04, Vol.14 (4), p.e1006089-e1006089

2018

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TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008653-e1008653

2021

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iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding

PLoS computational biology, 2020-07, Vol.16 (7), p.e1008040-e1008040

2020

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Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

PLoS computational biology, 2016-04, Vol.12 (4), p.e1004862-e1004862

2016

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A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro

PLoS computational biology, 2020-12, Vol.16 (12), p.e1008489

2020

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Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors

PLoS computational biology, 2017-08, Vol.13 (8), p.e1005678-e1005678

2017

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Transfer learning enables prediction of CYP2D6 haplotype function

PLoS computational biology, 2020-11, Vol.16 (11), p.e1008399

2020

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Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009820

2022

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Evaluation of residue-residue contact prediction methods: From retrospective to prospective

PLoS computational biology, 2021-05, Vol.17 (5), p.e1009027-e1009027

2021

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Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

PLoS computational biology, 2021-05, Vol.17 (5), p.e1008936

2021

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Tissue-guided LASSO for prediction of clinical drug response using preclinical samples

PLoS computational biology, 2020-01, Vol.16 (1), p.e1007607

2020

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Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing

PLoS computational biology, 2016-10, Vol.12 (10), p.e1005135-e1005135

2016

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Predicting protein targets for drug-like compounds using transcriptomics

PLoS computational biology, 2018-12, Vol.14 (12), p.e1006651-e1006651

2018

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Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

PLoS computational biology, 2021-09, Vol.17 (9), p.e1009384-e1009384

2021

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GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction

PLoS computational biology, 2021-06, Vol.17 (6), p.e1009048-e1009048

2021

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Full scale structural, mechanical and dynamical properties of HIV-1 liposomes

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009781-e1009781

2022

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Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins

PLoS computational biology, 2022-03, Vol.18 (3), p.e1009972-e1009972

2022

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Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008821

2021

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Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008857

2021

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ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients

PLoS computational biology, 2022-07, Vol.18 (7), p.e1010204-e1010204

2022

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NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT

PLoS computational biology, 2014-05, Vol.10 (5), p.e1003603-e1003603

2014

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BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach

PLoS computational biology, 2023-03, Vol.19 (3), p.e1011036-e1011036

2023

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Role of non-specific interactions in the phase-separation and maturation of macromolecules

PLoS computational biology, 2022-05, Vol.18 (5), p.e1010067-e1010067

2022

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A kinetic mechanism for enhanced selectivity of membrane transport

PLoS computational biology, 2020-07, Vol.16 (7), p.e1007789

2020

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

Propagating annotations of molecular networks using in silico fragmentation

TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations

iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors

Transfer learning enables prediction of CYP2D6 haplotype function

Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9

Evaluation of residue-residue contact prediction methods: From retrospective to prospective

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Tissue-guided LASSO for prediction of clinical drug response using preclinical samples

Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing

Predicting protein targets for drug-like compounds using transcriptomics

Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction

Full scale structural, mechanical and dynamical properties of HIV-1 liposomes

Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins

Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking

Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach

ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients

NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT

BiComp-DTA: Drug-target binding affinity prediction through complementary biological-related and compression-based featurization approach

Role of non-specific interactions in the phase-separation and maturation of macromolecules

A kinetic mechanism for enhanced selectivity of membrane transport

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