Molecular interaction networks in the analyses of sequence variation and proteomics data

Protein–protein interaction networks are typically generated in standard cell lines or model organisms as it is prohibitively difficult to record large interaction datasets from specific tissues or disease models at a reasonable pace. Although the interaction data are of high confidence, they thus do not reflect in vivo relationships as such. A wealth of physiologically relevant protein information, obtained under different conditions and from different systems, is available including information on genetic variation, protein levels, and PTMs. However, these data are difficult to assess comprehensively because the relationships between the entities remain elusive from the measurements. Here, we exemplarily highlight recent studies that gained deeper insight from genetic variation, protein, and PTM measurements using interaction information pointing toward the importance and potential of interaction networks for the interpretation of sequencing and proteomics data.     

一种变形表面的三维测量方法

提出一种新的利用标定图像进行三维测量的方法。利用SIFT算法找到初始的对应点,然后根据这些点生成三维空间中的种子点,再以这些种子点为中心,向外区域增长,直到完成整个物体表面测量。在每次增长的过程中,需要计算增长的三维空间平面在两个相机上的投影之间的图像相关系数。图像相关系数较大时认为是正确的增长,否则是错误的增长。实验证明,使用该方法能够得到很好的三维测量结果。     

CLARA算法聚类蛋白质序列的实现

随着基因工程产生大量新序列,导致蛋白质序列数据库的迅速增长,巨量蛋白质数据的功能组和族谱分析使蛋白质序列聚类分析成为结构和功能基因组学重要的研究目标,应用数据挖掘技术对生物数据进行聚类分析成为生物信息学研究的热点。聚类分析算法中的CLARA划分算法已广泛应用于其它领域,但在大数据量蛋白质序列聚类分析中应用很少,文章应用CLARA算法对在基准数据库中选取的蛋白质序列进行聚类分析,并将结果与其它几种蛋白质聚类算法进行了比较。     

暂态混沌神经网络在蛋白质关联图预测中应用研究

蛋白质结构预测是生物信息学的一个主要研究方向,而蛋白质关联图预测是其中的一个重要内容.针对蛋白质关联图预测问题,提出一种暂态混沌神经网络实现方法,所提出的方法具有暂态混沌特性和平稳收敛特性,能有效避免传统Hopfield 神经网络极易陷入局部极值的缺陷.它通过短暂的倒分叉过程,能很快进入稳定收敛状态.仿真结果表明:暂态混沌神经网络解决蛋白质关联图预测问题时,总能收敛到全局最优或几乎接近全局最优,同时具有更高的搜索效率.这种方法预测精度达到0.27,比随机预测器高9倍.     

蛋白质在硅烷膜表面吸附特性的压电传感监测

在压电石英晶片表面自组装修饰末端为胺基的硅烷膜,该膜在酸性和中性pH条件下带正电荷,可通过静电引力吸附带负电荷的牛血清白蛋白(BSA),吸附过程中的质量变化可通过石英晶片的谐振频率变化实时监测。结果表明:该吸附过程虽然为部分不可逆,但吸附等温线符合Langmuir方程,吸附速率常数为0.0117 L.g-1.s-1,吸附平衡常数为2.87 L.g-1,表观饱和吸附量Γ∞=0.954μg.cm-2。     

多特征融合的蛋白质相互作用位点预测

蛋白质相互作用位点预测为蛋白质功能和药物设计的理解提供重要线索。而蛋白质的各种特征为蛋白质相互作用位点预测提供了大量有用信息,特别是进化信息、残基序列邻近和空间邻近性。不同的蛋白质特征对蛋白质间的相互作用的贡献也不一样。通过提取蛋白质序列谱、保守性和残基熵,提出了特征融合技术对蛋白质相互作用位点进行研究,采用SVM构建三种预测器,分别对各种不同的特征加以验证,实验结果表明了基于特征融合方法的有效性和正确性。     

HClO对贻贝粘附单元DOPA氧化的理论研究

采用量子化学密度泛函理论(DFT)研究贻贝粘附单元DOPA(3,4-二羟基苯丙氨酸)的结构与性质,得分子的几何构型、原子电荷分布、反应活性及热力学等参数,表明:DOPA苯环易与HClO(次氯酸)发生亲电取代反应(1),生成3-氯4,5-二羟基苯丙氨酸,阻碍生成贻贝内超强粘附单元DOPA二联体,降低粘附蛋白间粘性;DOPA侧链易与HClO发生亲电亲核反应(2),促使DOPA侧链的断裂,降低粘附蛋白内粘性;在相同温度下,反应(1)和反应(2)的△G<0,且△G(1)<△G(2),反应(1)较易发生.     

Detecting Overlapping Community Structures in Networks

Community structure has been recognized as an important statistical feature of networked systems over the past decade. A lot of work has been done to discover isolated communities from a network, and the focus was on developing of algorithms with high quality and good performance. However, there is less work done on the discovery of overlapping community structure, even though it could better capture the nature of network in some real-world applications. For example, people are always provided with varying characteristics and interests, and are able to join very different communities in their social network. In this context, we present a novel overlapping community structures detecting algorithm which first finds the seed sets by the spectral partition and then extends them with a special random walks technique. At every expansion step, the modularity function Q is chosen to measure the expansion structures. The function has become one of the popular standards in community detecting and is defined in Newman and Girvan (Phys. Rev. 69:026113, 2004). We also give a theoretic analysis to the whole expansion process and prove that our algorithm gets the best community structures greedily. Extensive experiments are conducted in real-world networks with various sizes. The results show that overlapping is important to find the complete community structures and our method outperforms the C-means in quality.     

基于长周期光纤光栅的生物传感器设计及仿真

利用生物活性物质高效、专一的催化特性,通过生化反应中生成的复合物对包层折射率和半径的直接调制,提出了基于长周期光纤光栅的、可用于蛋白质等生物物质鉴别与分析的传感方案,并用数值计算方法对检测中所生成复合物薄膜层的折射率和厚度变化对耦合波长偏移和衰减的影响进行了仿真研究,为新型高灵敏度生物传感器的研发提供了理论依据。