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  database searching
     Based on the reported(0.165) nm high resolution crystal structure of spinach KARI complex,we obtained 279 molecules with low binding energy toward KARI from MDL/ACD 3D database searching with program DOCK 4.0,from which some compounds have been synthesized.
     在文献报道的菠菜KARI酶复合物0.165nm高分辨率晶体结构基础上,利用分子对接DOCK4.0方法进行MDL/ACD三维数据库搜寻,得到了279个与KARI酶结合能较低的小分子结构信息,并从中选取部分小分子进行化学合成,进而测试了其除草活性。
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     The results from both Southern blot analysis and database searching showed that it is a single copy gene in rice genome.
     Southern印迹杂交与水稻数据库搜寻的结果表明该基因在水稻基因组中是个单拷贝基因。
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     After analysis by SDS-PAGE and CapLC-MS/MS, totals of 135 proteins of rat hippocampal plasma membrane preparations were identified through database searching. Of the identified proteins, 70 were plasma membrane and membrane-associated proteins (accounting for 51.9 %), including Na+/K+-ATPase, Glutamate/aspartate transporter, Lipophilin, GLAST 1a and so on.
     一维SDSPAGE分离和CapLCMSMS分析后,通过数据库搜寻从大鼠海马组织细胞质膜样品中共鉴定出135种蛋白质,其中质膜蛋白和与膜相关的蛋白质共70种(占51.9%),主要包括Na+K+ATPase、谷氨酸天冬氨酸转运蛋白(glutamateaspartatetransporter)、亲脂素(lipophilin)、GLAST1a等.
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     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
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     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。
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  “数据库搜寻”译为未确定词的双语例句
     3D-Database Searching Based on the Crystal Structure of Ketol-acid Reductoisomerase (KARI) Complex
     基于酮醇酸还原异构酶KARI复合物晶体结构的三维数据库搜寻
短句来源
     Based on the reported crystal structure of complexes of the enzyme ketol-acid reductoisomerase (KARI), 279 molecules were obtained with predicted high affinity for KARI from MDL/ACD 3D-database searching, using program DOCK 4.0. The interaction pattern between some top-ranked molecules and KARI was described.
     以酮醇酸还原异构酶KARI复合物 0 165nm高分辨率晶体结构为基础 ,采用DOCK 4 0分子对接程序通过MDL/ACD三维数据库搜寻 ,找到了 2 79个与KARI结合能较低的小分子 ,讨论了能量打分较高分子同靶酶的作用模式 .
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     Peptide mass fingerprint (PMF) was the simplest and most direct, with its search results being easily influenced by parameter changes during the data process and database search.
     结果显示,三种搜寻法都能正确地鉴定该蛋白质,其中以利用MS数据的肽质量指纹谱搜寻法(PMF法)较为快捷方便,但鉴定结果易受数据处理和数据库搜寻鉴定时参数设置等因素影响;
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     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。
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     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)。
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  相似匹配句对
     Database
     数据库
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     TCM-informatics Study Based on 3D-database Searching
     基于三维数据库搜寻的中药信息学研究
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     Cryptograph Protection for Databases
     数据库的密码保护
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     Database of proteins is constructed for searching latent bioactive peptides encrypted in food proteins
     活性肽搜寻与蛋白模拟水解数据库的建立
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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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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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