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

S D'Souza, KV Prema, S Balaji - Drug Discovery Today, 2020 - Elsevier
Highlights•Chemical descriptors in modeling drug-target interaction.•Modeling approaches
in drug-target interaction prediction.•Machine learning and deep learning models in drug …

Interpretation of quantitative structure–activity relationship models: past, present, and future

P Polishchuk - Journal of Chemical Information and Modeling, 2017 - ACS Publications
This paper is an overview of the most significant and impactful interpretation approaches of
quantitative structure–activity relationship (QSAR) models, their development, and …

ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation

J Dong, DS Cao, HY Miao, S Liu, BC Deng… - Journal of …, 2015 - Springer
Background Molecular descriptors and fingerprints have been routinely used in QSAR/SAR
analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and …

Use of machine learning approaches for novel drug discovery

AN Lima, EA Philot, GHG Trossini… - Expert opinion on …, 2016 - Taylor & Francis
abstract Introduction: The use of computational tools in the early stages of drug development
has increased in recent decades. Machine learning (ML) approaches have been of special …

Comparing multiple machine learning algorithms and metrics for estrogen receptor binding prediction

DP Russo, KM Zorn, AM Clark, H Zhu… - Molecular …, 2018 - ACS Publications
Many chemicals that disrupt endocrine function have been linked to a variety of adverse
biological outcomes. However, screening for endocrine disruption using in vitro or in vivo …

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

J Dong, ZJ Yao, L Zhang, F Luo, Q Lin, AP Lu… - Journal of …, 2018 - Springer
Background With the increasing development of biotechnology and informatics technology,
publicly available data in chemistry and biology are undergoing explosive growth. Such …

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

H Atas Guvenilir, T Doğan - Journal of Cheminformatics, 2023 - Springer
The identification of drug/compound–target interactions (DTIs) constitutes the basis of drug
discovery, for which computational predictive approaches have been developed. As a …

Deep confidence: a computationally efficient framework for calculating reliable prediction errors for deep neural networks

I Cortés-Ciriano, A Bender - Journal of chemical information and …, 2018 - ACS Publications
Deep learning architectures have proved versatile in a number of drug discovery
applications, including the modeling of in vitro compound activity. While controlling for …

Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

I Cortés-Ciriano, QU Ain, V Subramanian… - …, 2015 - pubs.rsc.org
Proteochemometric (PCM) modelling is a computational method to model the bioactivity of
multiple ligands against multiple related protein targets simultaneously. Hence it has been …

Active learning for computational chemogenomics

D Reker, P Schneider, G Schneider… - Future medicinal …, 2017 - Taylor & Francis
Aim: Computational chemogenomics models the compound–protein interaction space,
typically for drug discovery, where existing methods predominantly either incorporate …