• 제목/요약/키워드: Template modeling

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Pharmacophore Modeling, Virtual Screening and Molecular Docking Studies for Identification of New Inverse Agonists of Human Histamine H1 Receptor

  • Thangapandian, Sundarapandian;Krishnamoorthy, Navaneethakrishnan;John, Shalini;Sakkiah, Sugunadevi;Lazar, Prettina;Lee, Yu-No;Lee, Keun-Woo
    • Bulletin of the Korean Chemical Society
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    • 제31권1호
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    • pp.52-58
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    • 2010
  • Human histamine H1 receptor (HHR1) is a G protein-coupled receptor and a primary target for antiallergic therapy. Here, the ligand-based three-dimensional pharmacophore models were built from a set of known HHR1 inverse agonists using HypoGen module of CATALYST software. All ten generated pharmacophore models consist of five essential features: hydrogen bond acceptor, ring aromatic, positive ionizable and two hydrophobic functions. Best model had a correlation coefficient of 0.854 for training set compounds and it was validated with an external test set with a high correlation value of 0.925. Using this model Maybridge database containing 60,000 compounds was screened for potential leads. A rigorous screening for drug-like compounds unveiled RH01692 and SPB00834, two novel molecules for HHR1 with good CATALYST fit and estimated activity values. The new lead molecules were docked into the active site of constructed HHR1 homology model based on recently crystallized squid rhodopsin as template. Both the hit compounds were found to have critical interactions with Glu177, Phe432 and other important amino acids. The interpretations of this study may effectively be deployed in designing of novel HHR1 inverse agonists.

조경 BIM 라이브러리 표준화를 위한 조경객체 및 속성정보 분류체계 (Landscape Object Classification and Attribute Information System for Standardizing Landscape BIM Library)

  • 김복영
    • 한국조경학회지
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    • 제51권2호
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    • pp.103-119
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    • 2023
  • BIM(건설정보모델링)을 건설사업 전반에 적용하려는 정부정책 이후 업계는 이를 적극적으로 도입, 활용하려는 동향을 보이고 있다. BIM 도입은 모델 객체들을 표준에 맞춰 라이브러리로 구축하여 반복 사용함으로써 업무량을 줄이고 데이터의 정합성과 호환성, 일관된 품질을 확보함으로써 촉진될 수 있다. 이에 국내 건축과 토목분야, 해외 조경분야에서는 이미 상당수의 BIM 라이브러리 표준화 연구를 수행하고 이를 토대로 지침을 마련하였다. 현재 국내 조경분야에서도 BIM에 관한 기초연구 및 도입을 시도하고 있으나 산업현장 적용에 어려움이 많아 확산이 지연되고 있다. 이는 표준화된 라이브러리 사용으로 BIM 설계업무의 효율성을 향상시킴으로써 개선될 수 있으므로 본 연구는 이에 대한 논의의 시발점을 마련함과 동시에 조경실무에서 라이브러리를 제작할 때 참고할 수 있는 객체의 기준을 제시하고자 하였다. 조경 BIM 라이브러리 표준화는 객체분류와 속성정보 도출이라는 두 가지 측면에서 모색되었다. 먼저 국내 건설정보분류체계, 물품분류체계, 조경설계기준, 조경공사표준시방서, 그리고 노르웨이 조경가협회의 BIM 객체분류체계를 참고로 객체분류를 시도하였다. 그 결과 조경객체는 조경식재, 조경시설물, 조경구조물, 조경포장재, 관수 및 배수시설의 5개 대분류하에 교목, 관목, 지피초화류, 옥외시설물, 옥외조명시설, 계단 및 경사로, 옥외벽체, 옥외구조물, 포장재, 경계석, 관수시설, 그리고 급배수시설을 포함하는 12개의 중분류로 나뉘었다. 다음으로 조경객체에 탑재될 속성정보를 도출하고 구조화하였다. 이를 위해 KBIMS(한국 BIM 표준)의 공통 속성정보를 항목에 포함하였고 객체의 종류에 따라 달라지는 객체 속성정보를 영국 조경협회의 PDT(제품정보 템플릿)를 참고하여 추가하였다. 이로써 공통 속성정보에 식별, 보급, 분류체계, 공급정보가 포함되었고, 객체 속성정보에 명명, 규격, 설치 또는 시공, 성능, 지속가능성, 유지관리에 관련된 정보들이 포함되었다. 본 연구는 조경객체의 라이브러리 표준화 방안을 제시함으로써 모델링의 업무 효율성 및 분야 간 BIM 모델의 데이터 정합성을 향상시킴으로써 조경 BIM 도입의 토대를 마련했다는 데에 의의가 있다.

가정간호사업 운용을 위한 정보전달체계 개발 I (가정간호 데이터베이스 구축과 뇌졸중 환자의 가정간호 전산개발) (Development of the Information Delivery System for the Home Nursing Service)

  • 박정호;김매자;홍경자;한경자;박성애;윤순녕;이인숙;조현;방경숙
    • 가정간호학회지
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    • 제4권
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    • pp.5-22
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    • 1997
  • The purpose of the study was to development an information delivery system for the home nursing service, to demonstrate and to evaluate the efficiency of it. The period of research conduct was from September 1996 to August 31, 1997. At the 1st stage to achieve the purpose, Firstly Assessment tool for the patients with cerebral vascular disease who have the first priority of HNS among the patients with various health problems at home was developed through literature review. Secondly, after identification of patient nursing problem by the home care nurse with the assessment tool, the patient's classification system developed by Park (1988) that was 128 nursing activities under 6 categories was used to identify the home care nurse's activities of the patient with CAV at home. The research team had several workshops with 5 clinical nurse experts to refine it. At last 110 nursing activities under 11 categories for the patients with CVA were derived. At the second stage, algorithms were developed to connect 110 nursing activities with the patient nursing problems identified by assessment tool. The computerizing process of the algorithms is as follows: These algorithms are realized with the computer program by use of the software engineering technique. The development is made by the prototyping method, which is the requirement analysis of the software specifications. The basic features of the usability, compatibility, adaptability and maintainability are taken into consideration. Particular emphasis is given to the efficient construction of the database. To enhance the database efficiency and to establish the structural cohesion, the data field is categorized with the weight of relevance to the particular disease. This approach permits the easy adaptability when numerous diseases are applied in the future. In paralleled with this, the expandability and maintainability is stressed through out the program development, which leads to the modular concept. However since the disease to be applied is increased in number as the project progress and since they are interrelated and coupled each other, the expand ability as well as maintainability should be considered with a big priority. Furthermore, since the system is to be synthesized with other medical systems in the future, these properties are very important. The prototype developed in this project is to be evaluated through the stage of system testing. There are various evaluation metrics such as cohesion, coupling and adaptability so on. But unfortunately, direct measurement of these metrics are very difficult, and accordingly, analytical and quantitative evaluations are almost impossible. Therefore, instead of the analytical evaluation, the experimental evaluation is to be applied through the test run by various users. This system testing will provide the viewpoint analysis of the user's level, and the detail and additional requirement specifications arising from user's real situation will be feedback into the system modeling. Also. the degree of freedom of the input and output will be improved, and the hardware limitation will be investigated. Upon the refining, the prototype system will be used as a design template. and will be used to develop the more extensive system. In detail. the relevant modules will be developed for the various diseases, and the module will be integrated by the macroscopic design process focusing on the inter modularity, generality of the database. and compatibility with other systems. The Home care Evaluation System is comprised of three main modules of : (1) General information on a patient, (2) General health status of a patient, and (3) Cerebrovascular disease patient. The general health status module has five sub modules of physical measurement, vitality, nursing, pharmaceutical description and emotional/cognition ability. The CVA patient module is divided into ten sub modules such as subjective sense, consciousness, memory and language pattern so on. The typical sub modules are described in appendix 3.

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Binding Mode Analysis of Bacillus subtilis Obg with Ribosomal Protein L13 through Computational Docking Study

  • Lee, Yu-No;Bang, Woo-Young;Kim, Song-Mi;Lazar, Prettina;Bahk, Jeong-Dong;Lee, Keun-Woo
    • Interdisciplinary Bio Central
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    • 제1권1호
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    • pp.3.1-3.6
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    • 2009
  • Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.