Fikriya, Zulfa Afiq (2019) Molecular Docking Senyawa Alkaloid SA2014 Terhadap Protein Cyclin D1 pada Kanker Menggunakan Firefly Algorithm. Masters thesis, Institut Teknologi Sepuluh Nopember.
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Abstract
Molecular docking atau penambatan ligan pada protein merupakan bidang komputasi yang sedang berkembang. Molecular docking dapat digunakan untuk mencari pola interaksi yang paling tepat antara protein reseptor dan ligan serta menjadi dasar penemuan dan desain obat berdasarkan struktur. Perkembangan dari metode dan algoritma docking yang efisien akan sangat berguna dalam penemuan obat secara simulasi. Firefly algorithm merupakan salah satu metode yang bisa digunakan untuk simulasi molecular docking. Firefly algorithm digunakan untuk mencari konformasi protein dan ligan yang optimal sehingga energi ikatan dari sistem secara keseluruhan diminimalkan. Dalam penelitian ini, digunakan dua kompleks protein-ligan dari Protein Data Bank (PDB) yaitu 2cpp dan 3ptb untuk menguji kemampuan algoritma. Didapatkan hasil bahwa firefly algorithm dapat digunakan untuk menyelesaikan molecular docking dengan nilai parameter pergerakan acak (α) sebesar 1.0. Kemudian algoritma ini digunakan untuk menyelesaikan molecular docking senyawa alkaloid SA2014 dari spons laut Cinachyrella anomala terhadap protein cyclin D1 pada kanker. Didapatkan hasil bahwa afinitas ligan SA2014 terhadap protein cyclin D1 lebih tinggi dibandingkan doxorubicin (sejenis obat kemoterapi) sehingga senyawa SA2014 memiliki potensi yang besar sebagai antikanker.
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Molecular docking or ligand binding in proteins is a developing field of computing. Molecular docking can be used to find the most appropriate interaction pattern between protein receptors and ligands and become the basis for the drug discovery and design based structures. The development of eficient docking methods and algorithms will be very useful in drug discovery simulation. Firefly algorithm is one of the method that can be used for molecular docking simulations. Firefly Algorithm is used to find the optimal conformation of proteins and ligands so that the binding energy of the whole system is minimized. In this research, two protein-ligand complexes from the Protein Data Bank (PDB), namely 2cpp and 3ptb were used to test the performance of the algorithm. The results show that the firefly algorithm can be used to solve molecular docking with random movement parameter (α) 1.0. Then this algorithm is used to solve molecular docking of alkaloid compounds SA2014 from Cinachyrella anomala sea sponges towards cyclin D1 protein in cancer. The results show that the SA2014 ligand affinity for cyclin D1 protein was higher than doxorubicin (a type of chemotherapy drug) so that the SA2014 compound had a great potential as an anticancer.
| Item Type: | Thesis (Masters) |
|---|---|
| Additional Information: | RTMa 615.19 Fik m-1 2019 |
| Uncontrolled Keywords: | firefly algorithm, molecular docking, penemuan obat, cyclin D1, alkaloid SA2014 |
| Subjects: | Q Science > Q Science (General) > Q337.3 Swarm intelligence Q Science > QA Mathematics Q Science > QA Mathematics > QA336 Artificial Intelligence Q Science > QA Mathematics > QA75 Electronic computers. Computer science. EDP |
| Divisions: | Faculty of Mathematics, Computation, and Data Science > Mathematics > 44101-(S2) Master Thesis |
| Depositing User: | Zulfa Afiq Fikriya |
| Date Deposited: | 13 Jan 2025 03:17 |
| Last Modified: | 13 Jan 2025 03:17 |
| URI: | http://repository.its.ac.id/id/eprint/66639 |
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