Graphical representation of biomolecules
In an effort to enhance the process of drug discovery and development, this work explores the possibility of creating an extensive and useful substructural-based chemical fingerprint for virtual drug screening by using differently sized subgraphs generated from biomolecule-converted graphs as...
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| Other Authors: | |
| Format: | Final Year Project (FYP) |
| Language: | English |
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Nanyang Technological University
2024
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| Online Access: | https://hdl.handle.net/10356/175620 |
| _version_ | 1826111285643706368 |
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| author | Su, Xinhui |
| author2 | Ke Yiping, Kelly |
| author_facet | Ke Yiping, Kelly Su, Xinhui |
| author_sort | Su, Xinhui |
| collection | NTU |
| description | In an effort to enhance the process of drug discovery and development, this work explores the
possibility of creating an extensive and useful substructural-based chemical fingerprint for virtual drug
screening by using differently sized subgraphs generated from biomolecule-converted graphs as
representative features. The experiment was done using data from ChEMBL, an open-source
chemical library, in the context of the BRAF protein and ligand, where the goal was to classify whether
a biomolecule is a BRAF ligand, with features being substructures within the biomolecule. The
effectiveness of the representation is evaluated through a classification task, where six models were
constructed, trained, and tested using the newly created representation. It was ultimately concluded
that using size 4 subgraphs as features produced the best results, and that the new representation
does have the potential to be used for virtual drug screening. |
| first_indexed | 2024-10-01T02:48:11Z |
| format | Final Year Project (FYP) |
| id | ntu-10356/175620 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T02:48:11Z |
| publishDate | 2024 |
| publisher | Nanyang Technological University |
| record_format | dspace |
| spelling | ntu-10356/1756202024-05-06T15:36:30Z Graphical representation of biomolecules Su, Xinhui Ke Yiping, Kelly Xiang Liming School of Physical and Mathematical Sciences A*STAR Bioinformatics Institute Lee Hwee Kuan LMXiang@ntu.edu.sg, ypke@ntu.edu.sg, leehk@bii.a-star.edu.sg Computer and Information Science Mathematical Sciences In an effort to enhance the process of drug discovery and development, this work explores the possibility of creating an extensive and useful substructural-based chemical fingerprint for virtual drug screening by using differently sized subgraphs generated from biomolecule-converted graphs as representative features. The experiment was done using data from ChEMBL, an open-source chemical library, in the context of the BRAF protein and ligand, where the goal was to classify whether a biomolecule is a BRAF ligand, with features being substructures within the biomolecule. The effectiveness of the representation is evaluated through a classification task, where six models were constructed, trained, and tested using the newly created representation. It was ultimately concluded that using size 4 subgraphs as features produced the best results, and that the new representation does have the potential to be used for virtual drug screening. Bachelor's degree 2024-05-02T00:22:12Z 2024-05-02T00:22:12Z 2024 Final Year Project (FYP) Su, X. (2024). Graphical representation of biomolecules. Final Year Project (FYP), Nanyang Technological University, Singapore. https://hdl.handle.net/10356/175620 https://hdl.handle.net/10356/175620 en application/pdf Nanyang Technological University |
| spellingShingle | Computer and Information Science Mathematical Sciences Su, Xinhui Graphical representation of biomolecules |
| title | Graphical representation of biomolecules |
| title_full | Graphical representation of biomolecules |
| title_fullStr | Graphical representation of biomolecules |
| title_full_unstemmed | Graphical representation of biomolecules |
| title_short | Graphical representation of biomolecules |
| title_sort | graphical representation of biomolecules |
| topic | Computer and Information Science Mathematical Sciences |
| url | https://hdl.handle.net/10356/175620 |
| work_keys_str_mv | AT suxinhui graphicalrepresentationofbiomolecules |