Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.
compound and bioactivity databases
deep learning
drug-target interactions
gold-standard data sets
ligand-based VS and proteochemometric modelling
machine learning
virtual screening
Journal
Briefings in bioinformatics
ISSN: 1477-4054
Titre abrégé: Brief Bioinform
Pays: England
ID NLM: 100912837
Informations de publication
Date de publication:
27 09 2019
27 09 2019
Historique:
received:
25
01
2018
revised:
25
05
2018
pubmed:
8
8
2018
medline:
22
7
2020
entrez:
8
8
2018
Statut:
ppublish
Résumé
The identification of interactions between drugs/compounds and their targets is crucial for the development of new drugs. In vitro screening experiments (i.e. bioassays) are frequently used for this purpose; however, experimental approaches are insufficient to explore novel drug-target interactions, mainly because of feasibility problems, as they are labour intensive, costly and time consuming. A computational field known as 'virtual screening' (VS) has emerged in the past decades to aid experimental drug discovery studies by statistically estimating unknown bio-interactions between compounds and biological targets. These methods use the physico-chemical and structural properties of compounds and/or target proteins along with the experimentally verified bio-interaction information to generate predictive models. Lately, sophisticated machine learning techniques are applied in VS to elevate the predictive performance. The objective of this study is to examine and discuss the recent applications of machine learning techniques in VS, including deep learning, which became highly popular after giving rise to epochal developments in the fields of computer vision and natural language processing. The past 3 years have witnessed an unprecedented amount of research studies considering the application of deep learning in biomedicine, including computational drug discovery. In this review, we first describe the main instruments of VS methods, including compound and protein features (i.e. representations and descriptors), frequently used libraries and toolkits for VS, bioactivity databases and gold-standard data sets for system training and benchmarking. We subsequently review recent VS studies with a strong emphasis on deep learning applications. Finally, we discuss the present state of the field, including the current challenges and suggest future directions. We believe that this survey will provide insight to the researchers working in the field of computational drug discovery in terms of comprehending and developing novel bio-prediction methods.
Identifiants
pubmed: 30084866
pii: 5062947
doi: 10.1093/bib/bby061
pmc: PMC6917215
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
1878-1912Subventions
Organisme : NHGRI NIH HHS
ID : U24 HG007822
Pays : United States
Informations de copyright
© The Author(s) 2018. Published by Oxford University Press.
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