Dissertation/ Thesis
Discovery of medicinal molecules based on similarity networks
| Title: | Discovery of medicinal molecules based on similarity networks |
|---|---|
| Authors: | D’Emanuele, Joseph |
| Publisher Information: | University of Malta Faculty of Information and Communication Technology. Department of Artificial Intelligence |
| Publication Year: | 2019 |
| Collection: | University of Malta: OAR@UM / L-Università ta' Malta |
| Subject Terms: | Big data, Ligands, Drug development -- Computer simulation |
| Description: | M.SC.ARTIFICIAL INTELLIGENCE ; At a molecular scale, ligands work by binding to a therapeutic target of interest, usually a protein, to solicit a response or block its function. Many modern drug discovery projects start with a computational search for these "active" molecules, called Virtual Screening (VS). Big data techniques are adequate for such problems that involve huge molecular datasets. In this dissertation we present a Ligand-Based Virtual Screening (LBVS) approach leveraging the parallelism and scalability of Apache Spark. We created multiple molecular similarity networks to discover new putative ligand binders for a given protein target, and to find other proteins which are likely to interact with a given ligand. For network abstraction weusedGraphFrames, which to our best knowledge, this is the first work that uses this approach for tackling VS problems. Weevaluatedwithsuccessourapproachby comparing its enrichment and recall with similar tools, using A Database of Useful Decoys: Enhanced(DUD-E)dataset. A web application for scientists was created to run in silico experiments using ChEMBL data and visualise the results. Finally, we used our web application to run a VS experiment to find putative targets for maltanedienol, which was not in our dataset. We correctly found oestrogen receptor and rejected farnesyl pyrophosphate synthase as protein targets, which were also confirmed via in vitro testing. ; N/A |
| Document Type: | master thesis |
| Language: | English |
| Relation: | D'Emanuele, J. (2019). Discovery of medicinal molecules based on similarity networks (Master's dissertation).; https://www.um.edu.mt/library/oar/handle/123456789/53065 |
| Availability: | https://www.um.edu.mt/library/oar/handle/123456789/53065 |
| Rights: | info:eu-repo/semantics/restrictedAccess ; The copyright of this work belongs to the author(s)/publisher. The rights of this work are as defined by the appropriate Copyright Legislation or as modified by any successive legislation. Users may access this work and can make use of the information contained in accordance with the Copyright Legislation provided that the author must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the prior permission of the copyright holder. |
| Accession Number: | edsbas.6E96B8D2 |
| Database: | BASE |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://www.um.edu.mt/library/oar/handle/123456789/53065# Name: EDS - BASE (ns324271) Category: fullText Text: View record from BASE |
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| RecordInfo | BibRecord: BibEntity: Languages: – Text: English Subjects: – SubjectFull: Big data Type: general – SubjectFull: Ligands Type: general – SubjectFull: Drug development -- Computer simulation Type: general Titles: – TitleFull: Discovery of medicinal molecules based on similarity networks Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: D’Emanuele, Joseph IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2019 Identifiers: – Type: issn-locals Value: edsbas |
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