TY - JOUR
T1 - Bat Algorithm for Solving Molecular Docking of Alkaloid Compound SA2014 Towards Cyclin D1 Protein in Cancer
AU - Fernando, Fedric
AU - Irawan, Mohammad Isa
AU - Fadlan, Arif
N1 - Publisher Copyright:
© Published under licence by IOP Publishing Ltd.
PY - 2019/11/7
Y1 - 2019/11/7
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85076125222&partnerID=8YFLogxK
U2 - 10.1088/1742-6596/1366/1/012089
DO - 10.1088/1742-6596/1366/1/012089
M3 - Conference article
AN - SCOPUS:85076125222
SN - 1742-6588
VL - 1366
JO - Journal of Physics: Conference Series
JF - Journal of Physics: Conference Series
IS - 1
M1 - 012089
T2 - 2nd International Conference on Applied and Industrial Mathematics and Statistics 2019, ICoAIMS 2019
Y2 - 23 July 2019 through 25 July 2019
ER -