Abstract

Bioinformatics is an interdisciplinary field that combines biology, computer science, information engineering, mathematics, and statistic to analyze and interpret biological data. Recently, bioinformatics had an important role in drug discovery. One of the steps for drug discovery is molecular docking. Molecular docking mimics the interaction between ligand and the target protein for in-vitro testing. Solving molecular docking problem isn't an easy task, because molecular docking involves many degrees of freedom. A lot of methods had been applied for this problem, one of them is artificial intelligence. This research will study the usage of bat algorithm in solving the molecular docking problem. Bat algorithm is an algorithm that uses the characteristic of the bats in searching prey. The research will solve the molecular docking of alkaloid compound SA2014 towards cyclin D1 protein in cancer. Alkaloid compound SA2014 is isolated from marine sponge Cinachyrella anomala. The objective function for this problem will be to minimize the binding energy, the lower energy means the bound of protein and ligand will be stronger. We use root mean squared deviation (RMSD) of protein structures to check the validation of bat algorithm. For validation, we used structure 3ptb and 2cpp. The validation shows that the bat algorithm is a valid method to solve the molecular docking problem because of the RMSD is not over 2Å and the free binding energy is negative. For docking SA2014 towards cyclin D1, bat algorithm shows a negative value -2.217.

Original languageEnglish
Article number012089
JournalJournal of Physics: Conference Series
Volume1366
Issue number1
DOIs
Publication statusPublished - 7 Nov 2019
Event2nd International Conference on Applied and Industrial Mathematics and Statistics 2019, ICoAIMS 2019 - Kuantan, Pahang, Malaysia
Duration: 23 Jul 201925 Jul 2019

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