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"ABSTRACTOne 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. "

"ABSTRACTMolecular Dynamics (MD) is one of processes that requires High Performance Computingenvironments to complete its jobs. In the preparation of virtual screening experiments, MD is one ofthe important processes particularly for tropical countries in searching for anti-Malaria drugs. Thesearch for anti-Malaria has previously conducted, for example by WISDOM project utilizing 1,700CPUS. This computing infrastructure will be one of the limitation for country like Indonesia that alsoneeds in silico anti malaria compounds searching from the country medical plants. Thus findingsuitable and affordable computing environment is very important. Our previous works showed that ourdedicated 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 computingenvironment on much better hardware specification of non dedicated Cluster computing and GPUTesla. We used two computing environments, the first one is Barrine HPC Cluster of The University ofQueensland which has 384 compute nodes with 3144 computing cores. The second one is Delta FutureGrid GPU Cluster which has 16 computing nodes with 192 computing cores, each nodes equippedwith 2 NVIDIA Tesla C2070 GPU (448 cores). The results show that running the experiment on adedicated computing power is much better than that on non dedicated ones, and the GPU performanceis still much better than that of Cluster."

"Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This text provides a presentation of this rapidly growing field"

"Senyawa yang berperan sebagai inhibitor HDAC kelas IIa telah banyak dikembangkan sebagai obat antikanker, antiinflamasi, penyakit Huntington, human papiloma virus dan antidiabetes. Senyawa inhibitor HDAC antara lain golongan hydroxamic acid, peptida siklik, asam alifatik dan benzamide. Metode yang digunakan untuk mencari senyawa inhibitor HDAC kelas IIa salah satunya adalah melalui pendekatan farmakofor 3D berbasis ligan. Senyawa aktif HDAC4 dan HDAC7 dibuat ke dalam dataset training dan test untuk pembuatan dan validasi model farmakofor 3D berbasis ligan menggunakan LigandScout 4.09.1. Model farmakofor terbaik digunakan untuk penapisan virtual terhadap database herbaldb. Senyawa hit yang diperoleh selanjutnya dilakukan penambatan molekul menggunakan AutoDock4Zn, simulasi dinamika molekuler dan perhitungan nilai MMGB/PBSA menggunakan AMBER12. Berdasarkan hasil validasi model farmakofor 3D berbasis ligan, dipilih model farmakofor terbaik yaitu model 6 dan 10 HDAC4 dan model 1 HDAC7. Berdasarkan hasil penapisan virtual diperoleh 6 senyawa hit yaitu artocarpesin, avicularin, dimboa glucoside, eriodictin, luteolin dan mirabijalone c. Proses simulasi dinamika molekul selama 10ns menunjukan bahwa senyawa yang memiliki aktivitas terbaik yaitu senyawa artocarpesin HDAC4 , mirabijalone c dan eriodictin HDAC7. Asam amino esensial HDAC4 meliputi Asp196, Asp290 dan His198 untuk interaksi ZBG. Asam amino esensial HDAC7 meliputi Asp707, Asp801 dan His709 untuk interaksi ZBG. ......Currently, compounds as the inhibitor of HDAC class IIa are developed as anticancer, antiinflammation, Huntington disease, human papilloma virus and antidiabetes. Inhibitor compounds of HDAC are mainly divided into hydroxamic acid, cyclic peptide, aliphatic acid and benzamide. 3D pharmacophore ligand based approached was used to found inhibitor compounds of HDAC class IIa. Active compounds of HDAC4 and HDAC7 were divided into training and test dataset for build and validation of 3D pharmacophore ligand based models using LigandScout 4.09.1. The best pharmacophore model, was used for virtual screening against herbaldb database. After this steps, hit compounds would be docking using AutoDock4Zn, molecular dynamic simulation, and MMGB PBSA calculation score using AMBER12. Based on the results of 3D model validation pharmacophore based ligand, selected models are models of best pharmacophore 6 and 10 HDAC4 and model 1 HDAC7. Based on the results of virtual screening, 6 hit compounds were obtained such as artocarpesin, avicularin, dimboa glucoside, eriodictin, luteolin and mirabijalone c. Molecular dynamics simulation process for 10ns indicate that the compound has the best activity are artocarpesin for HDAC4, mirabijalone c and eriodictin for HDAC7. Essential amino acids for HDAC4 include Asp196, Asp290 and His198 for ZBG interactions. Essential amino acids for HDAC7 include Asp707, Asp801 and His709 for ZBG interaction."