Investigating cardiotoxicity related with hERG channel blockers using molecular fingerprints and graph attention mechanism

POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability

(2022) Fengcheng Li et al.   BRIEFINGS IN BIOINFORMATICS

A deep learning method for predicting metabolite–disease associations via graph neural network

(2022) Feiyue Sun et al.   BRIEFINGS IN BIOINFORMATICS

Cell–cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies

(2022) Lihong Peng et al.   BRIEFINGS IN BIOINFORMATICS

ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA

(2022) Hanyu Zhang et al.   BRIEFINGS IN BIOINFORMATICS

LargeMetabo: an out-of-the-box tool for processing and analyzing large-scale metabolomic data

(2022) Qingxia Yang et al.   BRIEFINGS IN BIOINFORMATICS

Predicting the potential human lncRNA–miRNA interactions based on graph convolution network with conditional random field

(2022) Wenya Wang et al.   BRIEFINGS IN BIOINFORMATICS

Pharmacometabonomics: data processing and statistical analysis

(2021) Jianbo Fu et al.   BRIEFINGS IN BIOINFORMATICS

Predicting lncRNA–miRNA interactions based on interactome network and graphlet interaction

(2021) Li Zhang et al.   GENOMICS

Circular RNAs and complex diseases: from experimental results to computational models

(2021) Chun-Chun Wang et al.   BRIEFINGS IN BIOINFORMATICS

CardioTox net: a robust predictor for hERG channel blockade based on deep learning meta-feature ensembles

(2021) Abdul Karim et al.   Journal of Cheminformatics

Using Network Distance Analysis to Predict lncRNA–miRNA Interactions

(2021) Li Zhang et al.   Interdisciplinary Sciences-Computational Life Sciences

MDF-SA-DDI: predicting drug–drug interaction events based on multi-source drug fusion, multi-source feature fusion and transformer self-attention mechanism

(2021) Shenggeng Lin et al.   BRIEFINGS IN BIOINFORMATICS

VDA-RWLRLS: An anti-SARS-CoV-2 drug prioritizing framework combining an unbalanced bi-random walk and Laplacian regularized least squares

(2021) Ling Shen et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Optimization of metabolomic data processing using NOREVA

(2021) Jianbo Fu et al.   Nature Protocols

VARIDT 2.0: structural variability of drug transporter

(2021) Tingting Fu et al.   NUCLEIC ACIDS RESEARCH

DeepHIT: a deep learning framework for prediction of hERG-induced cardiotoxicity

(2020) Jae Yong Ryu et al.   BIOINFORMATICS

hERG-Att: Self-Attention-Based Deep Neural Network for Predicting hERG Blockers

(2020) Kim Hyunho et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction

(2020) Isidro Cortés-Ciriano et al.   Journal of Cheminformatics

Deep-belief network for predicting potential miRNA-disease associations

(2020) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

Prediction of hERG potassium channel blockage using ensemble learning methods and molecular fingerprints

(2020) Miao Liu et al.   TOXICOLOGY LETTERS

Deep Learning-Based Prediction of Drug-Induced Cardiotoxicity

(2019) Chuipu Cai et al.   Journal of Chemical Information and Modeling

FP2VEC: a new molecular featurizer for learning molecular properties

(2019) Woosung Jeon et al.   BIOINFORMATICS

Computational determination of hERG-related cardiotoxicity of drug candidates

(2019) Hyang-Mi Lee et al.   BMC BIOINFORMATICS

Molecular Docking Guided Grid-Independent Descriptor Analysis to Probe the Impact of Water Molecules on Conformational Changes of hERG Inhibitors in Drug Trapping Phenomenon

(2019) Saba Munawar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Chemi-Net: A Molecular Graph Convolutional Network for Accurate Drug Property Prediction

(2019) Ke Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Ensemble of decision tree reveals potential miRNA-disease associations

(2019) Xing Chen et al.   PLoS Computational Biology

Integrating Bipartite Network Projection and KATZ Measure to Identify Novel CircRNA-Disease Associations

(2019) Qi Zhao et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs

(2019) Tatsuki Negami et al.   Scientific Reports

NCMCMDA: miRNA–disease association prediction through neighborhood constraint matrix completion

(2019) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features

(2019) Yanyi Chu et al.   BRIEFINGS IN BIOINFORMATICS

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

(2018) Jie Dong et al.   Journal of Cheminformatics

Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs

(2018) Ying Hong Li et al.   BRIEFINGS IN BIOINFORMATICS

ADMET Evaluation in Drug Discovery. 16. Predicting hERG Blockers by Combining Multiple Pharmacophores and Machine Learning Approaches

(2016) Shuangquan Wang et al.   MOLECULAR PHARMACEUTICS

In silico prediction of hERG potassium channel blockage by chemical category approaches

(2016) Chen Zhang et al.   Toxicology Research

Computational investigations of hERG channel blockers: New insights and current predictive models

(2015) Bruno O. Villoutreix et al.   ADVANCED DRUG DELIVERY REVIEWS

Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity

(2015) Rodolpho C. Braga et al.   Molecular Informatics

ADMET Evaluation in Drug Discovery. 12. Development of Binary Classification Models for Prediction of hERG Potassium Channel Blockage

(2012) Sichao Wang et al.   MOLECULAR PHARMACEUTICS

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Role of hERG potassium channel assays in drug development

(2010) Birgit Priest et al.   Channels

Prospective Validation of a Comprehensive In silico hERG Model and its Applications to Commercial Compound and Drug Databases

(2010) Munikumar R. Doddareddy et al.   ChemMedChem

Extended-Connectivity Fingerprints

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

PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints

(2010) Chun Wei Yap   JOURNAL OF COMPUTATIONAL CHEMISTRY

Developing and validating predictive decision tree models from mining chemical structural fingerprints and high–throughput screening data in PubChem

(2008) Lianyi Han et al.   BMC BIOINFORMATICS