CSSP2 : An improved method for predicting contact-dependent secondary structure propensity

Yoon, Sukjoon,Welsh, Willian J,Jung, Heeyoung,Yoo, Young Do Research Institute of Women's Health Sookmyung Wom 2007 WOMEN And HEALTH Vol.3 No.1

The calculation of contact-dependent secondary structure propensity (CSSP) has been reported to sensitively detect non-native β-strand propensities in the core sequences of amyloidogenic proteins. Here we describe a noble energy-based CSSP method implemented on dual artificial neural networks that rapidly and accurately estimate the potential for the non-native secondary structure formation in local regions of protein sequences. In this method, we attempted to quantify long-range interaction patterns in diverse secondary structures by potential energy calculations and decomposition on a pairwise per-residue basis. The calculated energy parameters and seven-residue sequence information were used as inputs for artificial neural networks (ANNs) to predict sequence potential for secondary structure conversion. The trained single ANN using the >(i, i ± 4) interaction energy Parameter exhibited 74% accuracy in predicting the secondary structure of test sequences in their native energy state, while the dual ANN-based predictor using (i, i ± 4) and >(i, i ± 4) interaction energies showed 83% prediction accuracy. The present method provides a simple and accurate tool for predicting sequence potential for secondary structure conversions without using 3D structural information.

CSSP2: An improved method for predicting contact-dependent secondary structure propensity

Sukjoon Yoon,William J. Welsh,Heeyoung Jung,Young Do Yoo Sookmyung Women's University Research Institute of 2007 여성과 건강 Vol.3 No.1

From Confrontation to Conflict between China and Taiwan: Major Challenges for Taiwan’s Counter Strategy

( Sukjoon Yoon ),( Junho Yun ) 한국국방연구원 2020 The Korean Journal of Defense Analysis Vol.32 No.3

This article explores the issue of Taiwan’s security, increasingly threatened by China’s overwhelming military power. Taiwan has long been protected by a security commitment from the United States, but recent geopolitical shifts and technological developments have raised questions about the effectiveness of Taiwan’s strategy. Operational concepts and tactics, such as Taiwan’s A2/AD defense against the PLA are severely challenged by China’s enhanced amphibious capabilities. Taiwan now looks vulnerable to a full-scale amphibious assault by the PLA, and the U.S. commitment has been undermined by the transactional emphasis of the current administration, with Taiwan seen primarily as a tool to contain Chinese expansionism rather than an end in and of itself. Clearly, the Taiwanese military needs to up its game, and this article makes four recommendations: First, Taiwan should significantly increase its independent military capabilities, forcing Chinese military planners to reconsider whether the military options against Taiwan are worthwhile. Second, Taiwan should deploy its substantial technological prowess to strengthen its cyber warfare defenses. Third, Taiwan should rapidly acquire advanced foreign-made weapons and systems, abandoning its costly and timeconsuming indigenous development policies. Fourth, Taiwan’s leaders should give serious consideration to developing nuclear weapons, as only this can deter the Chinese military threat in the long term.

조수 유입구의 변형에 대한 현장관측과 수치모형의 적용 : field evidence and numerical simulation in the INDIA Project

강인철,윤석준 국민대학교 2002 北岳論叢 Vol.19 No.-

Tidal inlets are amongst the most dynamic geomorphological features along the worlds coastlines. Coastal erosion in and around tidal inlets due to natural migration, tidal flooding and storm events is commonly observed and frequently threatens adjacent communities and industry. Furthermore, inlets frequently connect the sea to sites of International ecological stature and/or areas of importance to tourism and therefore require careful management to maintain environmental quality. In total Europe spends around ￡150 million annually to offset the coastal erosion problems around inlets and in some European countries, as much as 50 % of the total annual budget for sea defences may be allocated to nourishment schemes at inlets(The Netherlands). In the USA over $100 million is spent annually simply to dredge some 75 million of 3 m sediment from inlet channels. In recognition of the environmentally sensitive nature of inlets and of an urgent requirement to improve present knowledge of inlet function, an international research project(INDIA) has examined the dynamics of a small natural tidal inlet in the Ri´a Formosa, Algarve, Portugal. Bringing together oceanographers, engineers, physicists, geologists and geographers from 20 Institutes worldwide, the project has used state-of-the-art field equipment to measure present day processes and a range of numerical models to extend the spatial and temporal range of the measurements. The paper outlines the project philosophy and structure and presents principal findings from field workers and numerical modelers. Underpinned by knowledge of inlet evolution over several years, and by knowledge of other inlet systems, a conceptual model describing the medium to long-term evolution of the present inlet is presented. Key elements of the model are then examined with reference to field observations and to numerical simulations of tides, waves, sediments and morphology. Supported by historical evidence of inlet evolution in the Ri´a Formosa, the picture that emerges of inlet dynamics from the present study is essentially one of relative simplicity and predictability in the short to medium-term. This emerging understanding of inlet function is then set against the known dynamics of other inlet systems in order to identify common processes and to identify key elements requiring further work.

The Regulatory Mechanism of the<i>LY6K</i>Gene Expression in Human Breast Cancer Cells

Kong, Hyun Kyung,Yoon, Sukjoon,Park, Jong Hoon American Society for Biochemistry and Molecular Bi 2012 The Journal of biological chemistry Vol.287 No.46

Somatic Mutaome Profile in Human Cancer Tissues

Kim, Nayoung,Hong, Yourae,Kwon, Doyoung,Yoon, Sukjoon Korea Genome Organization 2013 Genomics & informatics Vol.11 No.4

Somatic mutation is a major cause of cancer progression and varied responses of tumors against anticancer agents. Thus, we must obtain and characterize genome-wide mutational profiles in individual cancer subtypes. The Cancer Genome Atlas database includes large amounts of sequencing and omics data generated from diverse human cancer tissues. In the present study, we integrated and analyzed the exome sequencing data from ~3,000 tissue samples and summarized the major mutant genes in each of the diverse cancer subtypes and stages. Mutations were observed in most human genes (~23,000 genes) with low frequency from an analysis of 11 major cancer subtypes. The majority of tissue samples harbored 20-80 different mutant genes, on average. Lung cancer samples showed a greater number of mutations in diverse genes than other cancer subtypes. Only a few genes were mutated with over 5% frequency in tissue samples. Interestingly, mutation frequency was generally similar between non-metastatic and metastastic samples in most cancer subtypes. Among the 12 major mutations, the TP53, USH2A, TTN, and MUC16 genes were found to be frequent in most cancer types, while BRAF, FRG1B, PBRM1, and VHL showed lineage-specific mutation patterns. The present study provides a useful resource to understand the broad spectrum of mutation frequencies in various cancer types.

NDRG2 is involved in the oncogenic properties of renal cell carcinoma and its loss is a novel independent poor prognostic factor after nephrectomy.

Liang, Zhe Long,Kang, Kyeongah,Yoon, Sukjoon,Huang, Song Mei,Lim, Jae Sung,Kim, Jin Man,Lim, Jong-Seok,Lee, Hyo Jin Raven Press 2012 Annals of Surgical Oncology Vol.19 No.8

<P>Although NDRG2 is a candidate tumor suppressor, its exact role in renal cell carcinoma (RCC) is not fully understood. We investigated the functional role of NDRG2 and its clinical relevance in RCC tumorigenesis.</P>

Transposon-directed base-exchange mutagenesis (TDEM): a novel method for multiple-nucleotide substitutions within a target gene.

Kim, Yun Cheol,Lee, Hui Sun,Yoon, Sukjoon,Morrison, Sherie L Eaton Pub. Co 2009 Biotechniques Vol.46 No.7

<P>In this report we describe transposon-directed base-exchange mutagenesis (TDEM), an efficient and controllable method for introducing a mutation into a gene. Each round of TDEM can remove up to 11 base pairs from a randomly selected site within the target gene and replace them with any length of DNA of predetermined sequence. Therefore, the number of bases to be deleted and inserted can be independently regulated providing greater versatility than existing methods of transposon-based mutagenesis. Subsequently, multiple rounds of mutagenesis will provide a diverse mutant library that contains multiple mutations throughout the gene. Additionally, we developed a simple frame-checking procedure that eliminates nonfunctional mutants containing frameshifts or stop codons. As a proof of principle, we used TDEM to generate mutant lacZalpha lacking alpha-complementation activity and recovered active revertants using a second round of TDEM. Furthermore, a single round of TDEM yielded unique, inactive mutants of ccdB.</P>

1,3-Diphenyl-1H-pyrazole derivatives as a new series of potent PPARγ partial agonists

Choi, Jiwon;Park, Yunsun;Lee, Hui Sun;Yang, Young;Yoon, Sukjoon Sookmyung Women's University Research Institute of 2011 여성과 건강 Vol.6 No.2

A new series of PPARγ partial agonists, 1,3-diphenyl-1H-pyrazole derivatives, were identified using an improved virtual screening scheme combining ligand-centric and receptor-centric methods. An in vitro assay confirmed the nanomolar binding affinity of 1,3-diphenyl-1 H-pyrazole derivatives such as SP3415. We also characterized the competitive antagonism of SP3415 against rosiglitazone at micromolar concentrations. They showed a PPARγ partial agonistic activity similar to that of a known PPARγ drug, pioglitazone. in a cell-based transactivation assay. Furthermore, the structure-activity relationships of the pyrazole derivatives were investigated through comparative molecular field analysis and binding mode analysis, which provided new insight concerning their partial agonistic effect on PPARγ.

Constructing an Integrated Compound Library for Efficient Structure-based Virtual Screening

Lee, Hui Sun,Choi, Jiwon,Qinqin Ma,Ko, Yoonae,Yoon, Sukjoon Research Institute of Women's Health Sookmyung Wom 2007 WOMEN And HEALTH Vol.3 No.2

Structure-based virtual screening is now essential technique in early stage drug discovery. A critical infrastructure needed for structure-based virtual screening is a suitable, large scale and easy to access database of purchasable compounds. We have therefore built an integrated compound library for efficient structure-based virtual screening. Here, we present an overview of the library preparation Compounds collected from a variety of vendors as 2D SDfiles were converted into 3D structures containing all the hydrogen atoms. We merged all the 3D converted compounds into a single file and then filtered it to optimize the library for drug discovery usage. Moreover, we generated a conformer library of possible conformer structures for each compound in order to utilize it in ligand-centric virtual screening by shape matching. Our constructing integrated compound library can be applied to various steps of structure-based virtual screening and will contribute to enhancing the efficiency of the virtual screening for drug discovery.