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数据库搜寻
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  database searching
    Molecular dynamics was performed to minimize the HKOR model and to simulate the 3D-structure of Dyn8 based on the NMR results of dynorphin A( 1 - 14). The extracellular loops (EL) were built by self-constructed database searching.
    运用分子动力学优化HKOR模型并根据强啡肽A(1-14)核磁共振结果构建其三维结构,通过自建数据库搜寻建立HKOR的膜外环区。
短句来源
    In recent years, molecular docking has emerged as an imp ortant technology in the field of computer-aided drug research, includi ng database searching, combinatorial library design and protein-protein interaction investigation.
    近年来,分子对接方法已成为计算机辅助药物研究领域的一项重要技术,在数据库搜寻,组合库设计及蛋白作用研究方面得到了广泛发展。
短句来源
    In this review, recent advances in the area of computer aided drug design, such as active site analysis, database searching, de novo drug design and ligand scoring functions are discussed combined with some recent successful applications
    本文结合近年来若干成功应用实例 ,综述活性位点分析、数据库搜寻、全新药物设计、配体打分函数等计算机辅助药物设计技术的研究新进展
短句来源
  database searching
    Molecular dynamics was performed to minimize the HKOR model and to simulate the 3D-structure of Dyn8 based on the NMR results of dynorphin A( 1 - 14). The extracellular loops (EL) were built by self-constructed database searching.
    运用分子动力学优化HKOR模型并根据强啡肽A(1-14)核磁共振结果构建其三维结构,通过自建数据库搜寻建立HKOR的膜外环区。
短句来源
    In recent years, molecular docking has emerged as an imp ortant technology in the field of computer-aided drug research, includi ng database searching, combinatorial library design and protein-protein interaction investigation.
    近年来,分子对接方法已成为计算机辅助药物研究领域的一项重要技术,在数据库搜寻,组合库设计及蛋白作用研究方面得到了广泛发展。
短句来源
    In this review, recent advances in the area of computer aided drug design, such as active site analysis, database searching, de novo drug design and ligand scoring functions are discussed combined with some recent successful applications
    本文结合近年来若干成功应用实例 ,综述活性位点分析、数据库搜寻、全新药物设计、配体打分函数等计算机辅助药物设计技术的研究新进展
短句来源
  “数据库搜寻”译为未确定词的双语例句
    Two approaches in structure-based lead design can be distinguished: de novo design and searching three dimensional structures.
    基于结构的先导物设计主要有两种途径:全新设计(又称从头设计)和三维数据库搜寻
短句来源
    3D searching, compared to de novo design, can hardly find new structures according to pharmacophore and limited database though it can retrieve similar structures to known active compounds.
    限于“药效团”模型和数据库化合物,三维数据库搜寻可能发现活性已知的化合物的类似结构,与全新设计方法相比较,难以产生新结构类型和新的思想。
短句来源
    Almost all methods including de novo design and 3D database search are over concentrated on structure generation rather than quantitative evaluation of the binding properties of the newly produced molecule.
    目前几乎所有的全新设计(denovodesign)或3D数据库搜寻的方法都侧重于结构的生成而忽视了对结构的定量评价。
短句来源
    The structures of a new series of 1,5-diarylimidazole cycloxygenase-2 inhibitors were optimized using PM5 semiempirical quantum chemistry methods. The two-dimensional quantitative structure-activity elationships(2D-QSAR) of the inhibitors were derived by genetic algorithm and multiple regression methods using 430 literature or calculated structural pacameters.
    采用PM5半经验量子化学方法对29个新型1,5-二芳基咪唑类选择性环氧合酶(COX-2)抑制剂的结构进行了全优化,从数据库搜寻或计算了它们的430种结构参数,利用遗传算法和逐步回归方法,建立了经典结构-活性关系(2D-QSAR)。
短句来源
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  database searching
Database searching indicated thatsanA is homologous to the hypothetical methyltransferase inPyrococcus horikoshii with 25% identities and 41% positives.
      
Database searching indicated that the deduced protein ofsanB is homologous to the histidinol-phosphate aminotransferase inStreptomyces coelicolor with 31% identities and 47% positives.
      
MALDI-TOF-MS and Mascot database searching were exploited to identify these proteins.
      
Sequence database searching algorithms (e.g., Blitz, Fasta, Blast) are available for comparison of query to database sequences.
      
The proteins can be identified by database searching of the mass fingerprint of the intact peptides and of the characteristic fragment masses produced by tandem mass spectrometry.
      
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  database searching
Database searching indicated thatsanA is homologous to the hypothetical methyltransferase inPyrococcus horikoshii with 25% identities and 41% positives.
      
Database searching indicated that the deduced protein ofsanB is homologous to the histidinol-phosphate aminotransferase inStreptomyces coelicolor with 31% identities and 47% positives.
      
MALDI-TOF-MS and Mascot database searching were exploited to identify these proteins.
      
Sequence database searching algorithms (e.g., Blitz, Fasta, Blast) are available for comparison of query to database sequences.
      
The proteins can be identified by database searching of the mass fingerprint of the intact peptides and of the characteristic fragment masses produced by tandem mass spectrometry.
      
更多          


Fast and precise prediction of the receptor-ligand binding constant is an important aspect of structure-based drug design. Almost all de novo design methods or 3D database search methods tend to structure generation instead of structure evaluation. In this article, epididymal retinoic acid binding protein (ERABP) was used as a template to simulate the interaction between retinoids and their receptor. We deduced an equation predicting the drug-receptor binding constant. Furthermore, the conformers after docking...

Fast and precise prediction of the receptor-ligand binding constant is an important aspect of structure-based drug design. Almost all de novo design methods or 3D database search methods tend to structure generation instead of structure evaluation. In this article, epididymal retinoic acid binding protein (ERABP) was used as a template to simulate the interaction between retinoids and their receptor. We deduced an equation predicting the drug-receptor binding constant. Furthermore, the conformers after docking were used in CoMFA analysis to get a pharmacophore model of this series of compounds.

准确地预测配体-受体的结合常数是基于受体结构设计(structure-baseddesign)的一个重要方面。目前的全新设计(denovodesign)或3D数据库搜寻的方法大都侧重于结构的生成而对结构的定量评价有所忽视,本文以附睾维甲酸结合蛋白(ERABP)为模板,用DOCK程序研究了一组维甲类化合物与受体的相互作用,得到一个预测受体结合常数的方程。另外,对DOCK后的分子构象进行了CoMFA分析,得到这类化合物的作用模型。

Precise prediction of the binding constant of ligand to receptor is an important aspect of structure based drug design. Almost all methods including de novo design and 3D database search are over concentrated on structure generation rather than quantitative evaluation of the binding properties of the newly produced molecule. Using epididymal retinoic acid binding protein (ERABP) as a model, we simulated the interaction between retinoids and their receptor with DOCK program and obtained an equation for predicting...

Precise prediction of the binding constant of ligand to receptor is an important aspect of structure based drug design. Almost all methods including de novo design and 3D database search are over concentrated on structure generation rather than quantitative evaluation of the binding properties of the newly produced molecule. Using epididymal retinoic acid binding protein (ERABP) as a model, we simulated the interaction between retinoids and their receptor with DOCK program and obtained an equation for predicting the binding constants. According to the docking conformers of the ligands, CoMFA was also used to deduce a pharmacophoric model of this series of compound.

准确地预测配体受体的结合常数是基于受体结构设计(structurebaseddesign)的一个重要方面。目前几乎所有的全新设计(denovodesign)或3D数据库搜寻的方法都侧重于结构的生成而忽视了对结构的定量评价。本文以副睾维A酸结合蛋白(ERABP)为模板,用DOCK程序研究了一组维A类化合物与受体的相互作用,得到一个预测受体结合常数的方程。另外,对DOCK后的分子构象进行了CoMFA分析,得到这类化合物的作用模型。

To construct the 3D-structural model of human kappa opioid receptor (HKOR) and study its interacting mechanism with dynorphin A( 1 - 8) (Dyn8). METHODS: Comparative molecular modeling was applied to build the 7 transmembrane (TM) helical domain of HKOR using the bovine rhodopsin (OPSD) model as a template. Molecular dynamics was performed to minimize the HKOR model and to simulate the 3D-structure of Dyn8 based on the NMR results of dynorphin A( 1 - 14). The extracellular loops (EL) were built by self-constructed...

To construct the 3D-structural model of human kappa opioid receptor (HKOR) and study its interacting mechanism with dynorphin A( 1 - 8) (Dyn8). METHODS: Comparative molecular modeling was applied to build the 7 transmembrane (TM) helical domain of HKOR using the bovine rhodopsin (OPSD) model as a template. Molecular dynamics was performed to minimize the HKOR model and to simulate the 3D-structure of Dyn8 based on the NMR results of dynorphin A( 1 - 14). The extracellular loops (EL) were built by self-constructed database searching. D0CK4. 0 program was performed to construct Dyn8 complex with HKOR. RESULTS: (1) The model of HKOR was obtained and validated by theoretical and experimental data. (2) The Dyn8-HK0R interacting mechanism is reasonably explained; Side chain of residue Aspl38 interacts with pro-tonated nitrogen atom at the N-terminal residues of Dyn8 through electrostatic and hydrogen bonding, which play an important role in ligand binding with receptor. (3) Negatively charged amino acids in the second extracelluar loop (EL2) as Asp223 and Glu209 interact with the C-terminal positively charged residues in Dyn8, and Glu209 is a likely determinant of peptide ligand specificity. CONCLUSION: Some amino acid residues positioned in EL2, TM3, TM4, and TM5 form the binding site and therefore determine the selectivity of kappa peptide agonist.

目的:模建人Kappa阿片受体(HKOR)三维结构,并研究它与强啡肽A(1-8)(Dyn8)的相互作用机制。方法:以牛视紫红质(OPSD)为模板,运用比较分子模拟模建HKOR七段跨膜区的三维结构。运用分子动力学优化HKOR模型并根据强啡肽A(1-14)核磁共振结果构建其三维结构,通过自建数据库搜寻建立HKOR的膜外环区。应用DOCK4.0将强啡肽A(1-8)与HKOR进行对接。结果:(1)得到HKOR三维模型,并用理论及实验参数进行了校正。(2)合理解释了Dyn8-HKOR相互作用机制:Asp138通过与Dyn8的N端残基形成氢键及静电作用,在配体受体结合过程中起着重要的作用。(3)HKOR膜外第二环区(EL2)中带负电荷的氨基酸Asp223和Glu209与Dyn8的C端带正电荷的残基相互作用,而Glu209可能是决定肽类配体特异性的一个重要因素。结论:EL2,TM3,TM4,TM5上的一些关键氨基酸残基决定Kappa阿片受体与肽类配体的选择性结合。

 
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