• Journal of KIISE:Computing Practices and Letters
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• v.9 no.1
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• pp.25-32
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• 2003

As one of a new generation of industries, biotechnology is currently spotlighted, and is creating new research and industrial areas that can be readily combined with information technology. Among them, virtual screening is a method for new drug design which uses computer simulation to virtually design active drug candidates for special disease. In this paper, we present a distributed system for virtual screening, called DVSF(Distributed Virtual Screening Facilities). DVSF is designed and developed to perform virtual screening efficiently on logically distributed idle or strategic resources in a small or medium scale laboratory.

• Genomics & Informatics
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• v.5 no.1
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• pp.24-29
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• 2007

Computational virtual screening has become an essential platform of drug discovery for the efficient identification of active candidates. Moleculardocking, a key technology of receptor-centric virtual screening, is commonly used to predict the binding affinities of chemical compounds on target receptors. Despite the advancement and extensive application of these methods, substantial improvement is still required to increase their accuracy and time-efficiency. Here, we evaluate several advanced structure-based virtual screening approaches for elucidating the rank-order activity of chemical libraries, and the quantitative structureactivity relationship (QSAR). Our results show that the ensemble-average free energy estimation, including implicit solvation energy terms, significantly improves the hit enrichment of the virtual screening. We also demonstrate that the assignment of quantum mechanical-polarized (QM-polarized) partial charges to docked ligands contributes to the reproduction of the crystal pose of ligands in the docking and scoring procedure.

• Proceedings of the Korea Contents Association Conference
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• 2007.11a
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• pp.569-573
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• 2007

e-Science is a new paradigm to increase the research efficiency by applying the state-of-the-art information technology to the classical research methodology. Among the research fields influenced by e-Science, Biology and Bioinformatics are the fields that are using IT very actively. And virtual screening, a procedure for the drug discovery, is one of the bioinformatics applications which requires a large amount of computing resources. In this paper, WISDOM, which is a e-Science project to design a new drug for Malaria and Avian flu, and related projects are introduced and the joint research between KISTI and Chun-nam university planned for the virtual screening research is explained.

• Journal of KIISE:Computer Systems and Theory
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• v.35 no.6
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• pp.237-247
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• 2008

A virtual screening is the process of reducing an unmanageable number of compounds to a limited number of compounds for the target of interest by means of computational techniques such as molecular docking. And it is one of a large-scale scientific application that requires large computing power and data storage capability. Previous applications or softwares for molecular docking such as AutoDock, FlexX, Glide, DOCK, LigandFit, ViSION were developed to be run on a supercomputer, a workstation, or a cluster-computer. However the virtual screening using a supercomputer has a problem that a supercomputer is very expensive and the virtual screening using a workstation or a cluster-computer requires a long execution time. Thus we propose a service-based virtual screening system using Grid computing technology which supports a large data intensive operation. We constructed 3-dimensional chemical molecular database for virtual screening. And we designed a resource broker and a data broker for supporting efficient molecular docking service and proposed various services for virtual screening. We implemented service based virtual screening system with DOCK 5.0 and Globus 3.2 toolkit. Our system can reduce a timeline and cost of drug or new material design.

• Journal of Integrative Natural Science
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• v.15 no.4
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• pp.187-194
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• 2022

Protein Arginine Methyltransferase 5 (PRMT5), a significant member of the PRMT family, is a promising anticancer target. In this study, novel small compounds that act against the PRMT5 target are found by combining virtual screening with ChEMBL database medicines and Density Functional Theory. The ChEMBL database compounds were screened to retrieve the hit molecules, which further subjected for DFT analysis. Finally we have evaluated that ChEMBL- approved drugs such as Lifitegrast, Abiraterone acetate and Solifenacin may be potential inhibitors for PRMT5.

• Bulletin of the Korean Chemical Society
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• v.31 no.5
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• pp.1407-1410
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• 2010

• Bulletin of the Korean Chemical Society
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• v.32 no.11
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• pp.4086-4088
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• 2011

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3785-3787
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• 2010

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2655-2659
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• 2014

Dual specificity protein phosphatase 4 (DUSP4) has been considered a promising target for the development of therapeutics for various human cancers. Here, we report the first example for a successful application of the structure-based virtual screening to identify the novel small-molecule DUSP4 inhibitors. As a consequence of the virtual screening with the modified scoring function to include an effective molecular solvation free energy term, five micromolar DUSP4 inhibitors are found with the associated $IC_{50}$ values ranging from 3.5 to $10.8{\mu}M$. Because these newly identified inhibitors were also screened for having desirable physicochemical properties as a drug candidate, they may serve as a starting point of the structure-activity relationship study to optimize the medical efficacy. Structural features relevant to the stabilization of the new inhibitors in the active site of DUSP4 are discussed in detail.

• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.2006-2010
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• 2013

Leukocyte common antigen-related phosphatase (LAR) has been considered a promising target for the development of therapeutics for neurological diseases. Here, we report the first example for a successful application of the structure-based virtual screening to identify the novel small-molecule LAR inhibitors. Five of these inhibitors revealed micromolar inhibitory activities with the associated $IC_{50}$ values ranging from 2 to 6 ${\mu}M$. Because the newly identified inhibitors were also screened for having desirable physicochemical properties as a drug candidate, they may serve as a starting point of the structure-activity relationship study to optimize the medical efficacy. Structural features relevant to the stabilization of the new inhibitors in the active site of LAR are discussed in detail.