[HTML][HTML] A review on compound-protein interaction prediction methods: data, format, representation and model

S Lim, Y Lu, CY Cho, I Sung, J Kim, Y Kim… - Computational and …, 2021 - Elsevier
There has recently been a rapid progress in computational methods for determining protein
targets of small molecule drugs, which will be termed as compound protein interaction (CPI) …

Systems pharmacology in small molecular drug discovery

W Zhou, Y Wang, A Lu, G Zhang - International journal of molecular …, 2016 - mdpi.com
Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary
methods to create safe and effective medicines. Although considerable progress has been …

Interaction prediction in structure-based virtual screening using deep learning

A Gonczarek, JM Tomczak, S Zaręba, J Kaczmar… - Computers in biology …, 2018 - Elsevier
We introduce a deep learning architecture for structure-based virtual screening that
generates fixed-sized fingerprints of proteins and small molecules by applying learnable …

Predicting drug–target interactions with multi-information fusion

L Peng, B Liao, W Zhu, Z Li, K Li - IEEE journal of biomedical …, 2015 - ieeexplore.ieee.org
Identifying potential associations between drugs and targets is a critical prerequisite for
modern drug discovery and repurposing. However, predicting these associations is difficult …

Predicting drug–target interaction for new drugs using enhanced similarity measures and super-target clustering

JY Shi, SM Yiu, Y Li, HCM Leung, FYL Chin - Methods, 2015 - Elsevier
Predicting drug–target interaction using computational approaches is an important step in
drug discovery and repositioning. To predict whether there will be an interaction between a …

Deep learning from physicochemical information of concrete with an artificial language for property prediction and reaction discovery

S Mahjoubi, R Barhemat, W Meng, Y Bao - Resources, Conservation and …, 2023 - Elsevier
Existing machine learning-based approaches to investigate and design concrete mainly use
the mixture design variables to predict concrete properties and do not consider the …

Large-scale prediction of drug-target interaction: a data-centric review

T Cheng, M Hao, T Takeda, SH Bryant, Y Wang - The AAPS journal, 2017 - Springer
The prediction of drug-target interactions (DTIs) is of extraordinary significance to modern
drug discovery in terms of suggesting new drug candidates and repositioning old drugs …

A unified solution for different scenarios of predicting drug-target interactions via triple matrix factorization

JY Shi, AQ Zhang, SW Zhang, KT Mao, SM Yiu - BMC systems biology, 2018 - Springer
Background During the identification of potential candidates, computational prediction of
drug-target interactions (DTIs) is important to subsequent expensive validation in wet-lab …

Functional and DNA–protein binding studies of WRKY transcription factors and their expression analysis in response to biotic and abiotic stress in wheat (Triticum …

L Satapathy, D Kumar, M Kumar, K Mukhopadhyay - 3 Biotech, 2018 - Springer
WRKY, a plant-specific transcription factor family, plays vital roles in pathogen defense,
abiotic stress, and phytohormone signalling. Little is known about the roles and function of …

Laying in silico pipelines for drug repositioning: a paradigm in ensemble analysis for neurodegenerative diseases

N Dovrolis, G Kolios, G Spyrou, I Maroulakou - Drug discovery today, 2017 - Elsevier
Highlights•Computational drug repositioning is a serious support tool to shortlist candidate
drugs.•Up-to-date review of drug repositioning methodologies.•Example of a drug …