In silico methods and tools for drug discovery

B Shaker, S Ahmad, J Lee, C Jung, D Na - Computers in biology and …, 2021 - Elsevier
In the past, conventional drug discovery strategies have been successfully employed to
develop new drugs, but the process from lead identification to clinical trials takes more than …

Metabolomics for investigating physiological and pathophysiological processes

DS Wishart - Physiological reviews, 2019 - journals.physiology.org
Metabolomics uses advanced analytical chemistry techniques to enable the high-throughput
characterization of metabolites from cells, organs, tissues, or biofluids. The rapid growth in …

Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networking

Z Zhou, M Luo, H Zhang, Y Yin, Y Cai, ZJ Zhu - Nature Communications, 2022 - nature.com
Liquid chromatography-mass spectrometry (LC-MS) based untargeted metabolomics allows
to measure both known and unknown metabolites in the metabolome. However, unknown …

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

SX Ge, EW Son, R Yao - BMC bioinformatics, 2018 - Springer
Background RNA-seq is widely used for transcriptomic profiling, but the bioinformatics
analysis of resultant data can be time-consuming and challenging, especially for biologists …

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

AS Rifaioglu, H Atas, MJ Martin… - Briefings in …, 2019 - academic.oup.com
The identification of interactions between drugs/compounds and their targets is crucial for
the development of new drugs. In vitro screening experiments (ie bioassays) are frequently …

BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification

Y Djoumbou-Feunang, J Fiamoncini… - Journal of …, 2019 - Springer
Background A number of computational tools for metabolism prediction have been
developed over the last 20 years to predict the structures of small molecules undergoing …

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Y Djoumbou Feunang, R Eisner, C Knox… - Journal of …, 2016 - Springer
Background Scientists have long been driven by the desire to describe, organize, classify,
and compare objects using taxonomies and/or ontologies. In contrast to biology, geology …

The BioGRID interaction database: 2017 update

A Chatr-Aryamontri, R Oughtred, L Boucher… - Nucleic acids …, 2017 - academic.oup.com
Abstract The Biological General Repository for Interaction Datasets (BioGRID:
https://thebiogrid. org) is an open access database dedicated to the annotation and archival …

The contribution of the exposome to the burden of cardiovascular disease

T Münzel, M Sørensen, O Hahad… - Nature Reviews …, 2023 - nature.com
Large epidemiological and health impact assessment studies at the global scale, such as
the Global Burden of Disease project, indicate that chronic non-communicable diseases …

Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling

L Zhao, HL Ciallella, LM Aleksunes, H Zhu - Drug discovery today, 2020 - Elsevier
Highlights•Drug discovery has been advanced to a big data era with a large amount of
public data sources available.•Ten V features (volume, velocity, variety, veracity, validity …