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An atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re‐ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re‐ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone. Proteins 2013. © 2012 Wiley Periodicals, Inc. 相似文献
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Abstract: Since evidence is now available to support a nonendocrine autonomic function for thyrotropin-releasing hormone (TRH), quantitative measurements of TRH were made in nuclei of the vagal complex and other areas of the caudal medulla oblongata of the rat. Regions containing the dorsal motor nucleus of the vagus (DMN), nucleus tractus solitarius (NTS), hypoglossal nucleus, dorsal column nuclei, descending nucleus V (DNV), nucleus ambiguus (NA), raphe nuclei (MR) dorsomedial and ventromedial reticular formation, and inferior olivary nuclei were isolated from 300-μm-thick frozen sections of medulla by the micropunch technique. Each region was pooled bilaterally, homogenized in 0.1 M HCl, and vacuum-dried. Extracts were assayed for TRH by specific radioimmunoassay (RIA). TRH levels varied 100-fold among medulla nuclei. Highest content (ng/mg protein ± SEM) was found in DMN (14 ± 1.38) and NTS (4.7 ± 0.68), whereas lowest levels occurred in the DNV and MR (0.13, 0.06). Nearly 65% of the total medullary TRH was localized in nuclei associated with vagal complex (DMN, NTS, NA). Characterization of tissue immunoreactivity (TRHi) in these regions suggests the presence of TRH, since (1) medullary tissue extracts competed with 125I-TRH for antibody binding sites with the same affinity as authentic TRH; (2) TRHi in tissue extracts co-migrated with synthetic TRH when subjected to reverse-phase high performance liquid chromatography and Sephadex G-10 chromatography; and (3) rat serum TRH peptidases degraded TRHi and authentic TRH at similar rates. Another group of rats was subjected to unilateral (right side) vagotomy. At 33 weeks post-vagotomy, the vagal preganglionic cell population in the ipsilateral DMN was depleted 50–75%, while the contralateral side was unaffected. Interestingly, the content of TRH in the ipsilateral (right) DMN remained unchanged, whereas TRH in the contralateral DMN increased by 50%. In contrast, TRH was significantly elevated in the NA on the ipsilateral side of the lesion. TRH in both ipsi- and contralateral NTS was unchanged when compared with sham-operated controls. These results indicate that (1) TRH is present in several specific loci of the medulla; (2) very high levels are found in the vagal complex; and (3) vagotomy may alter TRH in the contralateral DMN and ipsilateral NA. 相似文献
34.
The Chemscore function was implemented as a scoring function for the protein-ligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, "Goldscore-CS" and "Chemscore-GS," in terms of docking accuracy, prediction of binding affinities, and speed. In the "Goldscore-CS" protocol, dockings produced with the Goldscore function are scored and ranked with the Chemscore function; in the "Chemscore-GS" protocol, dockings produced with the Chemscore function are scored and ranked with the Goldscore function. Comparisons were made for a "clean" set of 224 protein-ligand complexes, and for two subsets of this set, one for which the ligands are "drug-like," the other for which they are "fragment-like." For "drug-like" and "fragment-like" ligands, the docking accuracies obtained with Chemscore and Goldscore functions are similar. For larger ligands, Goldscore gives superior results. Docking with the Chemscore function is up to three times faster than docking with the Goldscore function. Both combined docking protocols give significant improvements in docking accuracy over the use of the Goldscore or Chemscore function alone. "Goldscore-CS" gives success rates of up to 81% (top-ranked GOLD solution within 2.0 A of the experimental binding mode) for the "clean list," but at the cost of long search times. For most virtual screening applications, "Chemscore-GS" seems optimal; search settings that give docking speeds of around 0.25-1.3 min/compound have success rates of about 78% for "drug-like" compounds and 85% for "fragment-like" compounds. In terms of producing binding energy estimates, the Goldscore function appears to perform better than the Chemscore function and the two consensus protocols, particularly for faster search settings. Even at docking speeds of around 1-2 min/compound, the Goldscore function predicts binding energies with a standard deviation of approximately 10.5 kJ/mol. 相似文献
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纤细裸藻(Euglena gracilis)是一类介于动物和植物之间的单细胞真核生物,在自然界中分布广泛。纤细裸藻兼具动植物细胞的特征,可进行光合自养、混养和异养培养,细胞内含有丰富的营养物质。近年来随着对纤细裸藻生物特性和胞内组分的深入研究,发现其在医药、食品以及饲料方面具有重要的应用价值,在提高免疫力、抗炎以及降低尿酸等方面的功效非常值得开发,特别是纤细裸藻特有的裸藻多糖等在生物医药领域具有广阔的应用前景。纤细裸藻作为食品原料、食品添加剂、饲料添加剂以及化妆品原料在国内外已经获得相关机构的认证,国外尤其是日本已经开发出系列产品。然而,国内对纤细裸藻的研究及开发还处于起步阶段,发展空间巨大,且目前关于纤细裸藻培养与功能研究及潜在的应用的综述报道较少。本文系统地介绍了纤细裸藻培养和生产的国内外研究现状,以及纤细裸藻粉与裸藻多糖活性功能的国内外研究结果,并对纤细裸藻应用开发存在的问题以及未来可能的发展方向进行了展望,为进一步建立和优化大规模且高效异养培养工艺、开发具有特定功能的纤细裸藻相关产品等提供科学依据。 相似文献
38.
为了探讨普氏蹄蝠下丘神经元在处理多普勒频移补偿后回声定位信号中的作用,实验采用双声刺激模式模拟蝙蝠不同飞行状态下产生多普勒频移补偿后的脉冲-回声对,即发声频率改变,回声频率维持恒定的情况下,研究下丘神经元对不同补偿值下的回声反应恢复率.结果发现:根据神经元在某一补偿值下对回声信号反应的恢复率是否超过70%,可将其分为具有选择性(S)和无选择性(NS)的两类神经元.且谐波内S神经元所占比例(68%)远超过非谐波内S神经元(39%).分析神经元的发放模式发现谐波内S神经元中相位型发放模式比例(44.3%)明显高于其他三种类型神经元.另外,虽然S和NS神经元的强度-潜伏期函数类型均以饱和型为主,但谐波内S神经元强度-潜伏期函数的最佳强度(best amplitude,BA)(95.3±14.0)dB SPL低于NS神经元的BA(104.1±10.2)d B SPL(P0.01),同时也低于非谐波内S神经元的BA(109.7±7.9)dB SPL(P0.01).以上实验结果表明,在下丘水平,神经元就已对多普勒频移补偿后回声定位信号的处理有了分工,集中在谐波内的S神经元通过提高对某一补偿值下回声信号反应的恢复率实现,对回声信息的精确编码,避免其他杂波干扰信息.同时,谐波内S神经元的发放模式和强度-潜伏期函数特点也满足其在复杂环境中精确声学成像的需求. 相似文献
39.
William A. Alexander 《Molecular simulation》2015,41(8):610-612
In a recent study of the Ar–CF4 intermolecular interaction potential [Shen C-C, Chang R-Y. Accurate ab initio calculation of the Ar–CF4 intermolecular potential energy surface. Mol Sim. 2010;36:1111–1122], Shen and Chang (SC) illustrated how the use of bond functions can improve the accuracy and basis-set saturation of electronic structure calculations employing perturbation and coupled-cluster theory. SC then used these ab initio data to derive analytic potential energy functions for use in chemical dynamics simulations. We critically examine these analytic potentials and comment on their usage in such simulations. Our analysis highlights the need for care and global validation when deriving analytic potential energy functions. 相似文献
40.
Sex assessment is key when investigating human remains either from medicolegal contexts or archaeological sites. Sex is usually assessed by examination of the skull and pelvis, but this may not always be possible if skeletal material is fragmented or incomplete. The present study investigated the potential for using carpals to assess sex, utilizing 100 individuals of known-sex from the Christ Church, Spitalfields Collection, curated at the Natural History Museum (London). A series of newly-defined measurements are applied to all eight carpals. Inter and intraobserver error tests show that all measurements are satisfactorily reproduced by the first author and another observer. Paired t-tests to investigate side asymmetry of the carpals reveal that some, but not all, measurements are consistently larger on the right hand side than the left. Independent t-tests confirm that all carpals are sexually dimorphic. Univariate measurements produce accuracy levels that range from 64.6 to 84.7%. Stepwise discriminant function analysis, devised separately for left and right sides, provides reliable methods for assessing sex from single and multiple carpals, with an accuracy range of 71.7 to 88.6%. All functions derived are tested for accuracy on a sample of 20 additional individuals from the Christ Church, Spitalfields Collection. 相似文献