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![Fig 2. Disconnected computational graph [8].](profile/Arry-Yanuar/publication/236737500/figure/fig1/AS:393097059029000@1470733050589/Disconnected-computational-graph-8_Q320.jpg)
IT based scientific research requires high computational resources. The
limitation on funding and infrastructure led the high performance computing era
from supercomputer to cluster and grid computing technology. Parallel
application running well on cluster computer as well as supercomputer, one of
the type is embarrassingly parallel application. M...
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Computational technology is an important thing that needed in the whole of human
life. Along with the development of computer technology, there are a significant data created
and wait to be processed; we will get more advantages if it well-processed, if not we will see the
data explosion, the data is just a useless stack. Research mitigates the oth...
Citations
... 128 This exploits the parallelism of shared memory hardware, such as multi-core CPU or multi-CPU workstations, 133 allowing to reach hyper linearity speedup on a multi-processor machine (or to be Embarrassingly Parallel [EP]). 134 Vina's amazing performance can be achieved thanks to the high independencies in each process. ...
Molecular simulations and molecular docking are widely used tools to investigate ligand/target interactions and in drug design. High‐performance computing (HPC) is boosting both the accuracy and predictive power of these approaches. With the advent of exascale computing, HPC may become standardly applied in many drug design campaigns and pharmacological applications. This review discusses how innovative HPC algorithms and hardware are being exploited in current simulations and docking codes, pointing also at some of the limitations of these approaches. The focus is on technical aspects which might not be all that familiar to the computational pharmacologist.
This article is categorized under:
• Software > Molecular Modeling
• Software > Simulation Methods
• Structure and Mechanism > Computational Biochemistry and Biophysics
Abstract
High‐performance computing in the upcoming exascale era will accelerate tremendously computer‐aided drug design.
... We developed the interfaces for this system -called SCloud [8]. This interface is built based on the cloud computing principal model that provides several services for the user such as on-demand self services, broad network access, resource pooling, rapid elasticity, and measured services. ...
The research on drug discovery has a long history. The research quality can be improved by using information technology as it can be used to model many aspects inside the process. Molecular dynamics is the first stage of the drug discovery process that models the finding of best conformation protein structure. The chosen structure is then used as a receptor for several datasets of ligand in virtual screening process. The main goal of this paper is developing an integrated computing platform for drug discovery research using "as a service" paradigm. Here, the cloud applications is used as a bridge between drug discovery tools that running on transparent multiplatform clients. This paper reports the results of the first from three phases of the research -the development of the computing platform interfaces and the analysis of several computing resources including the commercial cloud that will be used by the system.
