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September 28, 2016

Design of efficient computational workflows for in silico drug repurposing. Drug Discov Today.

Written and published by Biogerontology Research Foundation staff in collaboration with BioTime Inc., Insilico Medicine Inc. and Johns Hopkins University

Design of efficient computational workflows for in silico drug repurposing. Drug Discov Today. 2016 Sep 28. pii: S1359-6446(16)30343-9.

Vanhaelen Q(1), Mamoshina P(2), Aliper AM(2), Artemov A(2), Lezhnina K(2), Ozerov I(2), Labat I(3), Zhavoronkov A(2).

(1) Insilico Medicine Inc., Johns Hopkins University, ETC, B301, MD 21218, USA. Electronic address: vanhaelen@insilicomedicine.com.

(2) Insilico Medicine Inc., Johns Hopkins University, ETC, B301, MD 21218, USA.

(3) BioTime Inc., 1010 Atlantic Avenue, 102, Alameda, CA 94501, USA.

Abstract: Here, we provide a comprehensive overview of the current status of in silico repurposing methods by establishing links between current technological trends, data availability and characteristics of the algorithms used in these methods. Using the case of the computational repurposing of fasudil as an alternative autophagy enhancer, we suggest a generic modular organization of a repurposing workflow. We also review 3D structure-based, similarity-based, inference-based and machine learning (ML)-based methods. We summarize the advantages and disadvantages of these methods to emphasize three current technical challenges. We finish by discussing current directions of research, including possibilities offered by new methods, such as deep learning.

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