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Abstrak :
ABSTRACT
One of the processes requiring HPC environments is Molecular Dynamics ( MD ) . In tropical countries, the MD process is very important in the preparation of virtual screening experiments for anti-malaria search. Previous works on the virtual screening project for anti-malaria search conducted by WISDOM project uses grid infrastructure with 1,700 CPUs of various infrastructure provided in 15 countries [13]. In silico anti malaria compounds searching from Indonesian medical plants using virtual screening methods are urgently required. This can reduce the cost and time required compared to the direct searching or examining each compound by in vitro and in vivo which will spend a lot of time and expense . However, the use of thousands of processors is difficult for the researchers with limited resources in developing countries such as Indonesia. Our of previous studies using MD with GROMACS shows the improvement of the simulation time using Cluster. But that is not the case for some of our previous works with AMBER on Cluster where we did not obtain significant speed up. However, our previous works running GROMACS on GPUs provided significant speed up about 12 times faster than that run on Cluster. In this study , we build a GPU -based computing environment and have some MD simulation with AMBER. We used several computing environments such as cluster with 16 cores , GPU Geforce GTX 465 , GTX 470 , GTX 560 , GTX 680 , and GTX 780 . In addition to PfENR ( Plasmodium falciparum Enoyl acyl Carrier Protein Reductase ) enzyme , as benchmark we also conducted MD experiments on Myoglobin protein , Dihydrofolate reductase (DHFR) protein, and Ras - Raf protein . All experimental results showed that the slowest MD processes occurred on Cluster, followed in increasing order by GTX 560, GTX 465, GTX 470, GTX 680 and GTX 780. While the GPU speed up relative to cluster is about 24 , 26 , 32 , 24 , 77 and 101, respectively.

Abstrak :
ABSTRACT
Molecular Dynamics (MD) is one of processes that requires High Performance Computing environments to complete its jobs. In the preparation of virtual screening experiments, MD is one of the important processes particularly for tropical countries in searching for anti-Malaria drugs. The search for anti-Malaria has previously conducted, for example by WISDOM project utilizing 1,700 CPUS. This computing infrastructure will be one of the limitation for country like Indonesia that also needs in silico anti malaria compounds searching from the country medical plants. Thus finding suitable and affordable computing environment is very important. Our previous works showed that our dedicated Cluster computing power with 16 cores performance better than those using fewer cores, however the GPU GTX family computing power is much better. In this study, we investigate further our previous experiment in finding more suitable computing environment on much better hardware specification of non dedicated Cluster computing and GPU Tesla. We used two computing environments, the first one is Barrine HPC Cluster of The University of Queensland which has 384 compute nodes with 3144 computing cores. The second one is Delta Future Grid GPU Cluster which has 16 computing nodes with 192 computing cores, each nodes equipped with 2 NVIDIA Tesla C2070 GPU (448 cores). The results show that running the experiment on a dedicated computing power is much better than that on non dedicated ones, and the GPU performance is still much better than that of Cluster.

Abstrak :
The invention of graphical processing units (GPUs) has significantly improved the speed of long processes used in molecular dynamics (MD) to search for drug candidates to treat diseases, such as malaria. Previous work using a single GTX GPU showed considerable improvement compared to GPUs run in a cluster environment. In the current work, AMBER and dual GTX 780 and 970 GPUs were used to run an MD simulation on the Plasmodium falciparum enoyl-acyl carrier protein reductase enzyme; the results showed that performance was improved, particularly for molecules with a large number of atoms using single GPU.

Abstrak :
Potensi gas hidrogen untuk diimplementasikan sebagai pembawa energi tanpa emisi sangat menjanjikan. Namun ada beberapa kendala yang harus dihadapi dalam pengimplementasiannya, yakni pengembangan teknologi penyimpanan gas hidrogen. Penyimpanan gas hidrogen dalam suatu adsorben karbon nanostruktur seperti carbon nanotube menjadi salah satu pilihan untuk dapat meningkatkan kapasitas penyimpanannya. Namun, banyaknya penelitian eksperimen yang tidak memberikan hasil yang reproducible menyebabkan perlunya ada pengembangan penelitian teoritis adsorpsi gas hidrogen dengan pendekatan termodinamika molekuler. Dengan kalkulasi struktur elektronik ab initio, energi potensial interaksi antar molekul gas hidrogen diestimasi sebesar 0,099 kcal/mol dan antara gas hidrogen dengan carbon nanotube diestimasi sebesar 1,057 - 1,142 kcal/mol. Energi potensial tersebut direpresentasikan ke dalam persamaan nilai parameter potensial klasik sebagai fungsi dari diameter carbon nanotube agar didapatkan model potensial yang paling presisi. Setelah mendapatkan nilai-nilai parameter potensial interaksinya, simulasi dinamika molekuler dilakukan dengan ensemble canonical untuk menganalisa adsorpsi gas hidrogen pada permukaan luar carbon nanotube. Dari hasil pengolahan data simulasi dinamika molekuler, didapatkan bahwa kalor isosterik berkurang dari 1,6 kcal/mol hingga menjadi 0,2 kcal/mol pada kondisi permukaan adsorben jenuh. Hasil ini cukup sesuai dengan hasil penelitian eksperimental literatur lainnya. ......The potency of hydrogen gas to be implemented as energy carrier with zero emission is very promising. Unfortunately, there are still crucial problems on its implementation, one of them is the development of hydrogen storage technology. Storing hydrogen gas on nanostructured carbon adsorbent could be an alternative to improve the storage capacity. However, the fact that there were so many experimental researches that couldn?t provide reproducible results creates a need to develop theoritical research on hydrogen gas adsorption on carbon nanotube using moleculer thermodynamics approach. Using ab initio electronic structure calculations, The interaction potential energies between hydrogen molecules were estimated to be 0.099 kcal/mol and between hydrogen molecule and the outer surface of carbon nanotube were estimated to be 1.057 - 1.142 kcal/mol. The potential energies then were represented into an equation of potential parameter as a function of carbon nanotube diameterin order to get the most precise interaction potential model. Molecular dynamics simulations were performed on canonical ensemble to analyze hydrogen gas adsorption on outer surface of carbon nanotube. From our calculations results, the isosteric heat of hydrogen physical adsorption on carbon nanotube were estimated to be 1.6 kcal/mol and decreased to 0.2 kcal/mol on saturated surface condition. This results are acceptable with some previous experimental researches results.

Abstrak :
Krisis energi merupakan salah satu permasalahan serius yang dihadapi saat ini. Kebutuhan akan sumber energi yang dapat diperbaharui dan bebas dari polusi menjadikan hidrogen sebagai salah satu sumber energi alternatif yang sangat berpotensi untuk dikembangkan. Namun, dalam penggunaan hidrogen sebagai sumber energi masih menemui kendala dalam proses penyimpanannya. Yakni, membutuhkan tangki bertekanan tinggi atau disimpan dalam keadaan dicairkan hingga suhu cryogenik. Salah satu cara mengatasi kendala tersebut adalah dengan sistem adsorpsi. Carbon Nanotube (CNT) merupakan media penyimpan yang baik karena memiliki luas permukaan dan volume pori yang besar. Penelitian secara eksperimental umumnya masih memerlukan biaya yang mahal, maka perlu didukung metoda lain untuk menunjangnya seperti Simulasi Dinamika Molekular. Simulasi kali ini akan dilakukan dalam kondisi isotermis, dimana temperatur yang akan digunakan adalah 253 K, 273 K, dan 293 K pada tekanan yang bervariasi dari 1- 18 atm. Hasil simulasi menunjukkan temperatur 253 K memiliki kemampuan adsorpsi lebih baik dari temperatur lainnya. ......Energy crisis is one of the serious problems faced at present. The need for renewable energy sources and free of pollution makes hydrogen as one of alternative energy sources that are potentially to be developed. However, in the use of hydrogen as an energy source are still encountered obstacles in the process of storage. That is, the need of a high-pressure tank or stored in a liquified state to cryogenic temperature. One way of overcoming these barriers is by adsorption system. Carbon Nanotubes (CNT) is a storage medium that is good because it has a large surface area and large pore. Experimental research is generally still require a high cost, then it needs to be supported by other methods to support it as Molecular Dynamics Simulations. Simulation of this time will be performed in conditions of isotermis, where the temperature is to be used is 253 K, 273 K, and 293 K at a pressure varying from 1-18 atm. The result shows that temperature 253 K have better adsorption than the others.

Abstrak :
ABSTRAK
Deman dengue merupakan penyakit viral pada manusia yang disebabkan oleh infeksi virus dengue DENV . Infeksi ini pada beberapa orang juga dapat berkembang ke fase demam yang lebih akut yakni pada fase dengue hemorrhagic fever DHF dan dengue shock syndrome. DHF dan DSS dilaporkan menyebabkan 2,5 kematian dari 500.000 kasus klinis yang telah diketahi. Pengembangan antiviral untuk infeksi DENV seringkali mengalami kendala. Hal ini disebabkan karena DENV memiliki lebih dari satu jenis serotipe. Pengembangan sebuah antiviral yang dapat menangani infeksi dari semua jenis serotipe DENV sangatlah diperlukan. Antiviral ini dapat dikembangkan melalui inhibisi protein inang yang terlibat dalam siklus hidup DENV. Salah satu protein inang yang dapat dijadikan target adalah enzim ?-glucosidase I. Enzim ini memiliki peran penting dalam proeses pematangan envelope glikoprotein dari DENV. Pengembangan antiviral berbasis penautan fragmen secara in silico dapat menghasilkan kandidat obat terbarukan dengan afinitas pengikatan yang baik. Pada penelitan ini, senyawa kastenospermina telah ditautkan dengan fragmen potensial terbaik hasil simulasi penambatan pangkalan data fragmen. Hasil simulasi penambatan perpustakaan fragmen menunjukkan bahwa fragmen dengan nomor ID ZINC00549950 adalah kandidat terbaik untuk ditautkan dengan kastenospermina. Simulasi penautan kastenospermina dan fragmen ZINC00549950 dilakukan dengan MOE 2014.09. Penautan ini menghasilkan 127 ligan yang kemudian akan ditautkan kembali pada sisi aktif ?-glucosidase I. Hasil simulasi penambatan ini menunjukkan bahwa ligan dengan kode LRS 28 adalah ligan terbaik dari semua ligan termodifikasi dengan nilai ?Gbinding sebesar -53,8 Kkal/mol. Prediksi karakteristik drug-likeness dan toksisitas juga menunjukkan bahwa LRS 28 adalah kandidat antiviral yang baik sebagai inhibitor ?-glucosidase I. Hasil dinamika molecular juga menunjukkan bahwa komplek glu I dan LRS 28 cukup stabil pada temperature 310 K dan 312 K ditinjau dari nilai RMSD dan interaksi asam amino yang dibentuk pada akhir simulasi.

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ABSTRACT
Dengue fever is a viral disease in humans caused by dengue virus DENV infection. This infection in some people can also develop into a more acute phase of fever that known as dengue hemorrhagic fever DHF and dengue shock syndrome DSS . DHF and DSS are reported to causing 2.5 of deaths from the 500,000 clinical cases that have been reported. The development of antivirals for DENV infection is often constrained. This is occured because DENV has more than one type of serotype. The development of an antiviral that can cure the infection of all DENV serotypes is necessary. This antiviral can be developed through inhibition of host proteins involved in the DENV life cycle. One of the target host proteins is glucosidase I Glu I . This enzyme plays an important role in the proliferation of envelope glycoprotein of DENV. The development of antiviral based on fragment linking could generates novel drug candidates with good binding affinity. In this study, the castenospermine compound were linked with the best potential fragment from docking simulation of the fragment library. The docking simulation result of fragment library showed that fragment with ID number ZINC00549950 was the best candidate to link with castenospermine. The linking simulation between castenospermine and fragment ZINC00549950 was performed with MOE 2014.09. This linking generated 127 ligands which are then re docked to the active side of glucosidase I. The result of this re docking simulation showed that the LRS 28 ligand is the best ligand of all modified ligands with a value of Gbinding 53,8 Kcal mol. The drug likeness and toxicity properties prediction also showed that LRS 28 is a good antiviral candidate for glucosidase I inhibitor. The dynamic simulation indicated the LRS 28 and Glu I complex is stable enough based on RMSD value and protein receptor LRS 28 interaction that formed at the end of simulation.

Abstrak :
Kanker merupakan penyebab kematian utama di seluruh dunia. Salah satu faktor terjadinya kanker adalah modifikasi epigenetik yang abnormal (hipermetilasi). Hipermetilasi yang terjadi pada gen diyakini bahwa yang berperan besar dalam proses karsinogenesis adalah enzim DNA metiltransferase (DNMT). Penelitian-penelitian yang dilakukan saat ini untuk menemukan senyawa inhibitor DNMT dari bahan alam. Salah satu metode yang mendukung untuk analisis ini adalah metode in silico. Dalam penelitian ini, diteliti beberapa senyawa pilihan dari basis data herbal Indonesia hasil penapisan virtual terhadap aktivitasnya sebagai inhibitor DNMT. Hasil penambatan molekuler senyawa Cassiamin C, Procyanidin B2, Ent-epicatechin-4alpha-8-ent-epicatechin, Epicatechin-4beta-8-epicatechin-3-O-gallate, Neorhusflavanone, 3-O-galloylepigallocatechin-4beta-6-epicatechin-3-O-gallate, Withanolide, 3-O-galloylepigallocatechin-4beta-6-epigallocatechin-3-O-gallate, Cyanidin-3-6''-caffeylsophoroside-5-glucoside, Epifriedelinol, Gallo-catechin-4alpha-8-epicatechin, Scutellarein-7-glucosyl-1-4-rhamnoside, Epigallo-catechin-3-gallate (EGCG) (kontrol positif), dan sinefungin (kokristal) didapatkan nilai ΔG secara berturut-turut, -9.34, -10.95, -7.95, -11.01, -8.78, -8.87, -11.49, -7.98, -5.92, -8.92, -9.17, -8.76, -9.70, dan -9.11 kkal/mol. Senyawa cassiamin C, procyanidin B2, epicatechin-4beta-8-epicatechin-3-O-gallate, withanolide, dan gallocatechin-4alpha-8-epicatechin memiliki ΔG lebih rendah dari senyawa sinefungin (kokristal) dan EGCG (kontrol positif). Sehingga, tahap selanjutnya akan dilakukan simulasi dinamika molekuler terhadap tujuh ligan tersebut. Hasil simulasi dinamika molekuler menunjukkan aktivitas terbaik secara keseluruhan yaitu pada senyawa procyanidin B2, epicatechin-4beta-8-epicatechin-3-O-gallate, dan gallocatechin-4alpha-8-epicatechin. Residu asam amino yang penting bagi aktivitas inhibitor DNMT1 adalah Phe1145, Glu1168, Met1169, Cys1191, Glu1266, Ala1579, dan Val1580.

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Cancer is the leading cause of death worldwide. Factors of cancer is an abnormal epigenetic modifications (hypermethylation). Hypermethylation that occur in genes believed that played a major role in process of carcinogenesis is DNA methyltransferase (DNMT) enzyme. Recent studies is conducted to find DNMT inhibitor compounds from natural materials. Method that support for this analysis is in silico studies. In this study, several selected compounds from herbal database Indonesia results of virtual screening will be studying for the activity as an inhibitor DNMT. Results molecular docking of Cassiamin C, Procyanidin B2, Epicatechin-4alphaent-8-ent-epicatechin, Epicatechin-4beta-8-epicatechin-3-O-gallate, Neorhusflavanone, 3-O-galloylepigallocatechin-4beta-6-epicatechin-3-O-gallate, Withanolide, 3-O-galloylepigallocatechin-4beta-6-epigallocatechin-3-O-gallate, Cyanidin-3-6''-caffeylsophoroside-5-glucoside, Epifriedelinol, Gallocatechin-4alpha-8-epicatechin, Scutellarein-7-glucosyl-1-4-rhamnoside, Epigallocatechin-3-gallate (EGCG) (positive control), and Sinefungin (co-crystal) compounds, ΔG values obtained -9.34, -10.95, -7.95, -11.01, -8.78, -8.87, -11.49, -7.98, -5.92, -8.92, -9.17, -8.76, -9.70, and -9.11 kcal/mol, respectively. Cassiamin C, Procyanidin B2, Epicatechin-4beta-8-epicatechin-3-O-gallate, Withanolide, and Gallocatechin-4alpha-8-epicatechin compounds had lower ΔG than Sinefungin (co-crystal) and EGCG (positive control) compounds. Therefore, molecular dynamic simulation of seven selected compounds will be performed. The results of molecular dynamic simulation shows the best overall activity is Procyanidin B2, Epicatechin-4beta-8-epicatechin-3-O-gallate, and Gallocatechin-4alpha-8-epi-catechin compounds. Amino acid residues which are important for the activity of DNMT1 inhibitor is Phe1145, Glu1168, Met1169, Cys1191, Glu1266, Ala1579, and Val1580.

Abstrak :
Histon Deasetilase 2 (HDAC2) merupakan salah satu enzim dari suatu superfamily 18 enzim zinc-dependent yang kini tengah banyak diteliti sebagai target terapeutik. HDAC2 merupakan bagian dari HDAC kelas 1 yang diketahui memiliki aktivitas kuat sebagai katalis, dan umumnya merupakan target bagi inhibitor HDAC (HDACi). HDAC2 berperan pada gejala komplikasi akhir diabetes seperti nefropati diabetes. Sehingga penelitian lebih lanjut terkait inhibitor enzim-enzim HDAC khususnya HDAC2 perlu dikembangkan. Dalam penelitian ini, diteliti senyawa-senyawa dari basis data herbal Indonesia terhadap aktivitasnya sebagai inhibitor HDAC2, dengan melakukan penapisan virtual, untuk mendapatkan senyawa-senyawa pilihan, kemudian dilakukan simulasi dinamika molekuler untuk mengetahui interaksi senyawa sebagai inhibitor enzim. Didapatkan sepuluh besar peringkat senyawa penapisan virtual, kemudian diambil lima diantaranya dengan kriteria terbaik untuk dilakukan simulasi dinamika molekuler yaitu senyawa Boesenbergin B, Pongachalcone I, 6,8-Diprenylgenistein, Marmin, Mangostin, dengan kristal ligan N-(2-aminophenyl)benzamide sebagai kontrol positif, dengan nilai ΔG secara berturut-turut -8.28; -9.15; -7.05; -9.07; -7.15 dan ΔG kontrol positif -10.27. Dari simulasi dinamika molekuler diketahui aktivitas inhibitor HDAC2 berinteraksi pada residu asam amino penting yaitu His145C, Tyr308C, Zn379C, Leu276C, Phe155C, Phe210C, Leu144C, Met35C.

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Histone Deacetylase 2 (HDAC2) is one of a superfamily of 18 zinc-dependent enzymes, which now being widely investigated as therapeutic targets. HDAC2 is part of class I HDAC enzymes which knownly active as a strong catalys, and generally is the target for HDAC inhibitors (HDACi). HDAC2 play a role in the symptoms of late complications of diabetes such as diabetic nephropathy. So further research related to HDAC inhibitors, particularly HDAC2 need to be developed. In this study, research will be performed using virtual screening method to obtain several herbal compounds against their activities as HDAC2 inhibitors from the Indonesian herbal database, molecular dynamics simulations are then conducted to understand the interaction of compounds as inhibitors of the enzyme. The results of virtual screening process managed to obtained ten compounds with the highest Pharmacophore fit score rating, and would selected five compounds with the best criteria for molecular dynamics simulations, which are Boesenbergin B, Pongachalcone I, 6,8-Diprenylgenistein, Marmin, Mangostin, and active crytal ligand N-(2-aminophenyl)benzamide as a positive control, with respectively ΔG values obtained -8.28; -9.15; -7.05; -9.07; -7.15 and -10.27 as the ΔG value of active crystal ligand. From moleculer dynamics simulation of the activity of HDAC2 inhibitors are known to interact in two important amino acid residue that is His145C, Tyr308C, Zn379C, Leu276C, Phe155C, Phe210C, Leu144C, Met35C.