Judul: Meniran (Phyllanthus niruri) Potential as an Antivirus  against Foot and Mouth Disease In Silico
Abstrak: Penyakit mulut dan kuku (PMK) merupakan penyakit infeksius yang dapat menjangkiti hewan ternak sehingga mampu menyebabkan kerugian ekonomi yang masif. Meniran hijau (Phyllanthus niruri) diketahui memiliki aktivitas antivirus, sehingga dapat dijadikan salah satu alternatif antivirus PMK untuk diuji secara in silico. Penelitian diawali dengan berbagai analisis struktural dan fungsional reseptor target, penambatan molekuler dengan YASARA Structure, dan seleksi senyawa metabolit sekunder meniran hijau. Senyawa dengan nilai ΔG paling negatif dan Kd terkecil dikatakan memiliki ikatan terkuat, ini dapat dijumpai pada phyllanthenol dengan nilai ΔG dan Kd berturut-turut adalah -7.526 kkal/mol dan 2.261 μM. Namun, jika dilihat dari kemiripan letak pengikatan ligan pada struktur protein dengan rupintrivir sebagai ligan pembanding, kemungkinan besar eriodictin dan diosgenin dapat menjadi senyawa paling potensial. Berdasarkan pendekatan secara in silico pada penelitian ini, senyawa metabolit sekunder meniran hijau dapat dikatakan potensial sebagai antivirus PMK dengan metode kerja inhibisi protease 3Cnya., Foot and mouth disease (FMD) is an infectious disease that can infect livestock, causing massive economic losses. Green meniran (Phyllanthus niruri) is known to have antiviral activity, so it can be used as an alternative for FMD antiviral to be tested in silico. The research began with various structural and functional analyzes of target receptors, molecular docking with YASARA Structure, and selection of green meniran secondary metabolites. The compound with the most negative ΔG value and the smallest Kd is said to have the strongest bond, this can be found in phyllanthenol with ΔG and Kd values of -7.526 kcal/mol and 2.261 μM, respectively. However, judging from the similarity in the location of the binding of the ligand in the protein structure to that of rupintrivir as the comparison ligand, it is very likely that eriodictin and diosgenin could be the most potent compounds. Based on the in silico approach in this study, the secondary metabolites of green meniran can be said to be potential as FMD antivirals with their protease 3C inhibition method.
Keyword: antivirus, FMDV, inhibitor, green meniran, molecular docking

Judul: Molecular Docking of Turmeric (Curcuma longa) Active Compounds Against The FMD Virus RdRp Enzyme In Silico
Abstrak: Penyakit mulut dan kuku disebabkan oleh foot and mouth disease virus/FMDV, yaitu genus aphthovirus dari famili Picornaviridae. Replikasi genomnya sangat bergantung pada enzim RNA-dependent RNA-polymerase (RdRp). Penelitian ini bertujuan mencari senyawa aktif tanaman kunyit yang dapat menghambat aktivitas RdRp virus FMDV melalui penambatan molekuler secara in-silico. Bioavalibilitas ligan diprediksi berdasarkan karakteristik molekuler sesuai aturan Lipinski. Prediksi toksisitas ligan dilakukan menggunakan admetSAR. Reseptor diperoleh dari basis data PDB dengan ID 2E9R. Ligan uji berasal dari senyawa aktif rimpang kunyit. Ligan pembanding yang digunakan adalah ribavirin. Hasil screening menunjukkan senyawa utama golongan kurkuminoid memiliki energi bebas Gibbs (ΔG) yang rendah, yaitu siklokurkumin (-8.041 kkal/mol), kurkumin (-7.754 kkal/mol), demetoksikurkumin (-7.696 kkal/mol), dan bisdemetoksikurkumin (-7.506 kkal/mol). Simpulan penelitian ini adalah senyawa aktif kunyit memiliki potensi dalam menghambat aktivitas RdRp dari virus PMK., Foot and mouth disease is caused by foot and mouth disease virus/FMDV, an aphthovirus genus of the Picornaviridae family. Replication of its genome is highly dependent on RNA-dependent RNA-polymerase (RdRp). This study aims to find the active compound of the turmeric plant that can inhibit the RdRp activity of the FMDV virus through in-silico molecular docking. Ligand bioavailability was predicted based on molecular characteristics according to Lipinski's rule. Prediction of ligand toxicity was carried out using admetSAR. The receptor was obtained from the PDB database with ID 2E9R. The test ligands were derived from the active compound of turmeric rhizome. The comparative ligand used was ribavirin. The screening results showed that the main compounds from the Kurkuminoid group had low Gibbs free energy (ΔG), namely cyclocurcumin (-8.041 kcal/mol), curcumin (-7.754 kcal/mol), demethoxycurcumin (-7.696 kcal/mol), and bisdemethoxycurcumin (-7.506). kcal/mol). The conclusion of this study is that the turmeric’s active compound has potential to inhibit RdRp activity of FMD virus.
Keyword: foot and mouth diseases, RNA-dependent RNA-polymerase, turmeric

Judul: The Construction of Greedy SVP LLL Algorithm
Abstrak: A lattice is a set of all integer linear combination of a set of linearly independent vectors in ℝ𝑛���. The independent vectors are called bases of lattice. Any lattice can be generated from many bases, and these bases have the same cardinality. In the lattice, the most fundamental and renowned problem is the Shortest Vector Problem (SVP). SVP is a tracking problem of the shortest nonzero vector in a lattice with equivalent bases. In two dimensions, SVP problem has resolved exactly by Gauss’ algorithm. When the lattice dimension is higher than two, A.K. Lenstra, H.W. Lenstra and L. Lovasz gave a LLL algorithm to compute approximation of nonzero shortest vector in the lattice. Reduced bases solution obtained from LLL algorithm still be an approximation and has polynomial running time of arbitrary dimension which large enough. In 1994, Schnoor and Euchner modified this LLL algorithm as a new variant which later was named deep insertion LLL algorithm. This algorithm is a modified version of the LLL algorithm to the terms of the exchange step to improve the accuracy of output of LLL reduced bases and applying it to the subset sum problem. The purpose of this research are: (1) Reconstruct the LLL algorithm and deep insertion LLL algorithm using a geometric approach. (2) Construct a greedy SVP LLL algorithm. (3) Implement the three algorithms in a symbolic programming language, and evaluate them experimentally. A bases ℬ=[𝐛���1,𝐛���2,…,𝐛���𝑛���] in ℝ𝑚��� is called reduced LLL with parameter 𝛿��� if satisfies: (a) |𝜇���𝑗���𝑖���|≤12, for every integer 𝑖���,𝑗��� with 1≤𝑖���<𝑗���<𝑛���. (b)𝛿���‖𝜋���𝑗���(𝐛���𝑗���)‖2≤‖𝜋���𝑗���(𝐛���𝑗���+1)‖2, for 𝑗���=1,2,…,𝑛���−1,where 𝛿��� is a reduced parameter of real numbers with 14<𝛿���<1. The first requirement is the reduced basis 𝛿��� must “nearly orthogonal” and in its computation case, this requirement can be reached out by using the Gram-Schmidt’s orthogonalization. While the second requirement is called exchange step, or used to called as Lovasz condition. By using both of these requirements, then they establish the LLL algorithm. Then, Schnoor and Euchner modify the LLL algorithm based on the requirements of the exchange step called the deep insertion LLL algorithm, where the exchange step is based on the comparison of the projected vector in orthogonal complement [𝐛���1,𝐛���2,…,𝐛���𝑘���−1]⊥ after j-th reduction. To construct greedy SVP LLL algorithm, the requirements of the exchange step is based on purely by comparing norm of lattice 𝐛���𝑗��� with norm lattice 𝐛���𝑖��� for 𝑖���=1,2,3…,𝑗���−1. The process of insertion reduced vector after the exchange step also has done greedily. Then, we calculate the number of arithmetic operation in greedy SVP LLL algorithm for further analysis. The result of our exprimentation for three algorithms on the certain matrix size shows that the running time of the three algorithms increases propotional to the size of the matrix. The result also shows that by using 𝛿���=34 for the LLL algorithm and the deep insertion LLL algorithm, and the greedy SVP LLL algorithm which is a new variant made by using no parameter of 𝛿���, outperform of the other of two previous algorithm in terms of speed with the same output.
Keyword: LLL algorithm, LLL deep insertion algorithm, greedy SVP LLL algorithm