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181.
De novo structure prediction can be defined as a search in conformational space under the guidance of an energy function. The most successful de novo structure prediction methods, such as Rosetta, assemble the fragments from known structures to reduce the search space. Therefore, the fragment quality is an important factor in structure prediction. In our study, a method is proposed to generate a new set of fragments from the lowest energy de novo models. These fragments were subsequently used to predict the next‐round of models. In a benchmark of 30 proteins, the new set of fragments showed better performance when used to predict de novo structures. The lowest energy model predicted using our method was closer to native structure than Rosetta for 22 proteins. Following a similar trend, the best model among top five lowest energy models predicted using our method was closer to native structure than Rosetta for 20 proteins. In addition, our experiment showed that the C‐alpha root mean square deviation was improved from 5.99 to 5.03 Å on average compared to Rosetta when the lowest energy models were picked as the best predicted models. Proteins 2014; 82:2240–2252. © 2014 Wiley Periodicals, Inc. 相似文献
182.
基于叶片的过氧化物酶(POD)、超氧化物歧化酶(SOD)及花蕾的酯酶(EST)同工酶酶谱的聚丙烯酰胺凝胶电泳(PAGE)分析,对32份辣椒种质的遗传多样性进行了研究。结果表明:(1)共产生29种谱带,其中POD谱带13种234条,多态性位点比例(PPL)和相对迁移率(Rf)变化范围分别为50.0%~80.0%和0.05~0.69;SOD谱带8种140条,PPL、Rf分别为100.0%、0.38~0.88;EST谱带8种163条,PPL、Rf分别为50.0%~87.5%、0.16~0.89。(2)共发现多态位点26个,PPL、总基因频率(Pt)、等位基因平均数(A)、Nei基因多样性指数(He)、Shannon信息指数(SII)、平均遗传一致度(GI)和遗传距离(GD)分别为89.66%、0.578 7、1.896 6、0.272 2、0.415 2、0.736 6和0.314 3;32份辣椒材料的Jaccard遗传相似系数为0.348~0.905,并聚类为4个栽培种群。(3)4个栽培种群内基因多样度(HS)为0.143 6;种群间基因多样度(DST)、基因分化系数(GST)、GI和GD分别为0.149 4、0.51、0.784 4和0.246 6。(4)9份紫色辣椒种质共发现多态位点16个,PPL、Pt、A、He、SII、GI和GD分别为55.17%、0.611 1、1.551 7、0.194 1、0.291 9、0.781 6和0.249 4。研究认为,32份辣椒材料的总体、栽培种间和种内以及紫色材料间遗传分化程度大,为紫色辣椒杂交育种的亲本选配与绿色品种的遗传改良提供了参考依据。 相似文献
183.
不同采收期裸花紫珠的HPLC指纹图谱研究 总被引:1,自引:0,他引:1
为建立裸花紫珠药材高效液相指纹图谱研究方法,该研究采用0.4%磷酸水溶液(A)-乙腈(B);梯度洗脱为0~15 min,16%~25% B,15~25 min,25%~39.7% B;Agilent ZORBAX SB-C18色谱柱(4.6 mm×250 mm,5μm);柱温为30℃;流速为1 mL??min-1;进样量为10μL;检测波长327 nm;检测时间25 min 等色谱条件,研究了不同采集时间共25批裸花紫珠药材的指纹图谱,获取14个共有特征色谱峰,确定了其中的3个成分,利用相似度分析、主成分分析及对应分析对它们进行了分析.结果表明:HPLC 指纹图谱结合计量分析法可有效评价裸花紫珠的质量,该方法可有效应用到裸花紫珠原料及其制品的质量控制中. 相似文献
184.
Edwin C. M. Mariman F. G. Bouwman Erik E. J. G. Aller Marleen A. van Baak Ping Wang 《Genes & nutrition》2014,9(3)
Relatively rare variants with a moderate-to-high biological effect may contribute to the genetic predisposition of common disorders. To investigate this for obesity, we performed exome sequencing for 30 young (mean age: 29.7 years) extremely obese Caucasian subjects (mean body mass index: 51.1 kg/m2; m/f = 11/29). Rare variants with a moderate-to-high predicted biological effect were assembled and subjected to functional clustering analysis. It showed that the 55 clustered protocadherin genes on chromosome 5q31 have a significantly (P = 0.002) higher frequency of rare variants than a set of 325 reference genes. Since the protocadherin genes are expressed in the hypothalamus, we tested another 167 genes related to the function of the hypothalamus, but in those genes, the frequency of rare variants was not different from that of the reference genes. To verify the relation of variation in the protocadherin genes with extreme obesity, we analyzed data from more than 4,000 European Americans present on the Exome Variant Server, representing a sample of the general population. The significant enrichment of rare variants in the protocadherin genes was only observed with the group of extremely obese individuals but not in the “general population”, indicating an association between rare variants in the protocadherin cluster genes and extreme obesity. 相似文献
185.
《Journal for Nature Conservation》2014,22(5):462-470
A systematic approach for prioritization of protected areas is the use of artificial intelligence. This approach employs computer algorithms based on an objective function to identify the best network of areas to be protected. Site selection algorithms are commonly used to identify areas of high conservation value. This study used three types of heuristic algorithms (simulated annealing, greedy, rarity) to prioritize areas for protection in Mazandaran Province of Iran using Marxan software. The goal was to select a conservation network with the smallest possible area in which maximum protection targets are achievable. The effects of spatial scale, algorithm, and zone compactness were also examined. We found that the existing network of protected areas is inadequate to achieve conservation targets. The algorithm results provided the best areas for supplementation of the current network. The simulated annealing algorithm provided the most plausible results for all scenarios. These results can be used to modify the existing boundaries of the protected areas network and introduce new sites for protection of plant and animal species. 相似文献
186.
基因芯片技术为疾病异质性研究提供了有力的工具。当前基于传统聚类分析的方法一般利用芯片上大量基因作为特征来发现疾病的亚型, 因此它们没有考虑到特征中包含的大量无关基因会掩盖有意义的疾病样本的分割。为了避免这个缺点, 提出了基于耦合双向聚类的异质性分析方法(Heterogeneous Analysis Based on Coupled Two-Way Clustering, HCTWC)来搜索有意义的基因簇以便发现样本的内在分割。该方法被应用于弥漫性大B细胞淋巴瘤(diffuse large B-cell lymphoma DLBCL)芯片数据集, 通过识别的基因簇作为特征对DLBCL样本聚类发现生存期分别为55%和25%的两类DLBCL亚型(P<0.05), 因此, HCTWC方法在解决疾病异质性是有效的。 相似文献
187.
188.
Distribution of plant functional attributes in a managed forest in relation to neighbourhood structure 总被引:1,自引:0,他引:1
The importance of neighbourhood structure on the distribution of plant functional attributes was investigated in two managed forests in Denmark. Species composition was recorded for 325 plots of 5×5 m and species were assigned to functional groups based on vegetative attributes: (a) Raunkiaer life-form and (b) height of adult plants, and regenerative attributes: (c) mode of dispersal and (d) pollination class. The distribution of attributes was related to neighbourhood parameters that reflect the composition, distribution and diversity of nine habitat classes within a 25-m radius from the focal plot. Regression trees were used to analyse counts of attributes per plot. Best predictors were neighbourhood scores for open areas, road-side habitat, and neighbourhood diversity. The correlation between individual functional attributes and neighbourhood parameters were presented in a correlation matrix. A cluster analysis, representing a first step towards the construction of plant functional types, resulted in five groups characterised by a particular combination of functional attributes and preference of neighbourhood. 相似文献
189.
优良的甘蔗原料是生产高品质红糖的基础,筛选营养价值丰富的甘蔗种质资源,是选育红糖加工型甘蔗品种的基础.本研究以全国广泛种植、当前普遍用于红糖加工以及历史上较早应用于制作红糖等具有代表性的16份甘蔗种质为试验材料,通过分析蔗汁的蛋白质、总游离氨基酸、总多酚、蔗糖、还原糖、灰分、氯化物、胶体含量等营养、品质指标,采用因子分... 相似文献
190.