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FP-Zernike:An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 111-119页

作者： junhai qi Chenjie Feng Yulin Shi Jianyi Yang Fa Zhang Guojun Li Renmin Han Research Center for Mathematics and Interdisciplinary Sciences Shandong UniversityQingdao 266237China BioMap Research Menlo ParkCA 94025USA College of Medical Information and Engineering Ningxia Medical UniversityYinchuan 750004China Institute of Engineering Medicine Beijing Institute of TechnologyBeijing 100081China

The release of AlphaFold2 has sparked a rapid expansion in protein model *** protein structure retrieval is crucial for the analysis of structure models,while measuring the similarity between structures is the key challenge in structural *** existing structure alignment algorithms can address this challenge,they are often ***,the state-of-the-art approach involves converting protein structures into three-dimensional(3D)Zernike descriptors and assessing similarity using Euclidean ***,the methods for computing 3D Zernike descriptors mainly rely on structural surfaces and are predominantly web-based,thus limiting their application in studying custom *** overcome this limitation,we developed FP-Zernike,a user-friendly toolkit for computing different types of Zernike descriptors based on feature *** simply need to enter a single line of command to calculate the Zernike descriptors of all structures in customized ***-Zernike outperforms the leading method in terms of retrieval accuracy and binary classification accuracy across diverse benchmark *** addition,we showed the application of FP-Zernike in the construction of the descriptor database and the protocol used for the Protein Data Bank(PDB)dataset to facilitate the local deployment of this tool for interested *** demonstration contained 590,685 structures,and at this scale,our system required only 4-9 s to complete a *** experiments confirmed that it achieved the state-of-the-art accuracy ***-Zernike is an open-source toolkit,with the source code and related data accessible at https://***/biocode/tools/BT007365/releases/0.1,as well as through a webserver at http://***/.

关键词： Zernike descriptor Structure alignment PDB dataset Open-source Retrieval system

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Design and Synthesis of Tri-substituted Chiral Pyrrolidin-2-one Derivatives as CCR4 Antagonists

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Chinese Journal of Chemistry 2013年第9期31卷 1144-1152页

作者： Wei Sun Linjie Tian Hui qi Dan Jiang Ying Wang Song Li junhai Xiao Xiaohong Yang School of Pharmaceutical Sciences Jilin University Changchun Jilin 130021 China Laboratory of Computer-Aided Drug Design & Discovery Beijing Institute of Pharmacology & Toxicology Beij'ing 100850 China Center for Human Disease Genomics Peking University Beijing 100083 China

A series of tri-substituted chiral pyrrolidin-2-one derivatives have been designed and synthesized as CC chemokine receptor 4 （CCR4） antagonists. The structure of CCR4 was built by homology modeling. Asymmetric synthesis was applied to synthesize the R,R configuration chiral pyrrolidin-2-one scaffold. The stereoisomeric con- figurations of the compounds were identified by 2D I H-~H COSY spectroscopy and 1D NOESY spectroscopy. This method was more economical and convenient than traditional X-ray single crystal diffraction. In addition, the inter- actions between these compounds and the N-terminal extracellular tail of CCR4 were studied using capillary zone electrophoresis. The CCR4 chemotaxis inhibition effect was tested in CCR4-transfected HEK293 cells. Several compounds showed potent activities as CCR4 antagonists. Among these compounds, lc is the most active one. Its apparent binding constant of CZE experiment result is （1.569±0.11）× 10s L·mol ^-1, and its percentage inhibition of the HEK293/CCR4 cells migration with the concentration of I gmol·L ^-1 in DMSO is 59%. And compound If has slightly higher affinity to N-terminal of CCR4 according to its apparent binding constant than lb because of the in- troduced ester linkage. Further studies on the mechanism of these compounds are in progress.

关键词： CCR4 antagonists tri-substituted chiral pyrrolidin-2-one derivatives synthesis

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Construction of poly-naphthalocyanine linked by [4]-radialene-like structures on silver surfaces

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Nano Research 2021年第12期14卷 4563-4568页

作者： Rongting Wu De-Liang Bao Linghao Yan junhai Ren Yanfang Zhang qi Zheng Ye-Liang Wang qing Huan Shixuan Du Hong-Jun Gao Present address:Department of Applied Physics Yale UniversityNew Haven06511USA Institute of Physics&University of Chinese Academy of Sciences Chinese Academy of SciencesBeijing100190China CAS Center for Excellence in Topological Quantum Computation Chinese Academy of SciencesBeijing100190China Songshan Lake Materials Laboratory Dongguan523808China

Cyclic-conjugated linkages between planar-macrocydic molecules contribute to the robustness of the two-dimensional (2D) polymerization and extension of π-interactions. The fabrication of such linkages in 2D polymers remains challenging. Combining scanning tunneling microscope (STM) measurements and density functional theory (DFT) calculations, we demonstrate a linear polymerization of metal-free naphthalocyanine (NPc) molecules with [4]-radialene-like linkages on silver surfaces. Experimentally, by depositing NPc molecules on the Ag(110) surface and subsequent annealing up to 750 K, one-dimensional polymers are constructed along the [\(1\overline 1 0\)] direction. High-resolution STM images show a stem-leaf-like feature. STM simulations based on a linear polymer of NPc molecules linked by four-membered carbon rings, [4]-radialene-like structure, agree well with the experimental observations. DFT calculations reveal that the polymerization process includes detaching two-terminal H atoms of NPc molecules along [\(1\overline 1 0\)] direction, then bonding with a neighboring dehydrogenated NPc molecule by forming a four-membered ring. The dehydrogenation process can be promoted by on-surface impurities such as additional H atoms. Similar polymerizations have been achieved on Ag(111) surfaces in an amorphous way. Moreover, the energy gap of the NPc molecule decreases after linear polymerization, suggesting a red-shift for its optical absorption/scattering spectrum. Our study offers a new route to polymerize conjugated molecules with extended planar π-interactions.

关键词： polymerization naphthalocyanine π-interaction extension scanning tunneling microscope density functional theory calculation

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基于运动约束的脉冲雷达游标测距方法

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北京航空航天大学学报 2015年第2期41卷 331-336页

作者：陈浩郭军海齐巍北京跟踪与通信技术研究所北京100094

为解决传统脉冲雷达游标测距中解相位模糊和解速度模糊相互耦合的问题,将目标的运动约束与传统游标测距结合在一起,提出了一种新的基于运动约束的游标测距方法.利用运动约束积累一段时间的观测数据进行UKF滤波,得到精度较高的径向速度... 详细信息

为解决传统脉冲雷达游标测距中解相位模糊和解速度模糊相互耦合的问题,将目标的运动约束与传统游标测距结合在一起,提出了一种新的基于运动约束的游标测距方法.利用运动约束积累一段时间的观测数据进行UKF滤波,得到精度较高的径向速度来解速度模糊,得到的无模糊速度可用于距离游标.利用得到的游标距离取代脉冲测距数据进行UKF预测,可准确估计下一时刻的速度并解速度模糊,这样建立了可同时解相位模糊和解速度模糊的耦合滤波器,成功实现脉冲雷达游标测距,并大大减小脉冲雷达测距随机误差.高速飞行器主动段仿真和脉冲雷达实测数据验证表明,该算法能大大减小径向距离随机误差,将距离随机误差减少一个数量级至分米级.

关键词：距离游标运动约束解相位模糊解速度模糊 UKF滤波

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基于经验小波变换的目标加速度估计算法

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北京航空航天大学学报 2015年第1期41卷 154-159页

作者：陈浩郭军海齐巍北京跟踪与通信技术研究所北京100094

加速度会使目标回波信号的频谱展宽甚至偏移,使传统脉冲雷达测速方法不能准确估计信号的多普勒频率.为了克服目标的加速度对脉冲雷达测速的影响,提出了一种基于经验小波变换(EWT)的径向加速度估计算法.对回波信号进行EWT变换和能量型频... 详细信息

加速度会使目标回波信号的频谱展宽甚至偏移,使传统脉冲雷达测速方法不能准确估计信号的多普勒频率.为了克服目标的加速度对脉冲雷达测速的影响,提出了一种基于经验小波变换(EWT)的径向加速度估计算法.对回波信号进行EWT变换和能量型频率主成分提取方法得到回波信号瞬时频率,并利用抗差最小二乘拟合得到相位高阶系数,进而估计目标径向加速度.利用估计的加速度对信号频谱进行补偿就能准确估计信号的多普勒频率.仿真表明EWT方法是一种高精度快速算法,且估计误差最接近待估参数的C-R下界.实测高速飞行器脉冲雷达I/Q数据验证表明,EWT算法估计的加速度精度优于0.4 m/s2.该算法可应用于脉冲雷达实时加速度估计.

关键词：径向加速度非平稳信号经验小波变换瞬时频率频率提取

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倾斜煤层条带煤柱留设宽度统一解

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采矿与安全工程学报 2019年第2期36卷 248-255页

作者：张常光祁航赵均海蔡明明长安大学建筑工程学院陕西西安710061

我国倾斜煤层可采储量占比较大,但至今鲜有针对倾斜煤层条带煤柱的计算方法。基于统一强度理论,考虑中间主应力、矸石支撑作用和煤层倾角的影响,建立倾斜煤层条带煤柱留设宽度的统一解,对其进行可比性分析与对比验证,探讨矸石的支撑作... 详细信息

我国倾斜煤层可采储量占比较大,但至今鲜有针对倾斜煤层条带煤柱的计算方法。基于统一强度理论,考虑中间主应力、矸石支撑作用和煤层倾角的影响,建立倾斜煤层条带煤柱留设宽度的统一解,对其进行可比性分析与对比验证,探讨矸石的支撑作用和各参数的影响特性。研究结果表明:本文所得留设宽度统一解是一系列有序理论解答的集合,可退化为多种强度准则解答,并得到文献经验公式的验证,具有广泛的理论意义和工程应用前景;矸石支撑作用对浅埋煤层、煤层开采宽度较大时的影响较大,加以利用可提高煤层的采出率;留设宽度随煤层倾角的增加而减小,特别是煤层倾角大于10°时,当作水平煤层的设计将偏于保守;应合理考虑煤柱强度的中间主应力效应和煤层界面强度参数的变化。

关键词：倾斜煤层条带煤柱统一强度理论垮落矸石留设宽度

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FBXL4 serves as a clock output molecule to regulate sleep through promoting GABAA receptor degradation

FBXL4 serves as a clock output molecule to regulate sleep th...

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中国神经科学学会第十二届全国学术会议

作者： qian LI Yi LI Xiao WANG Junxia qi Huawei TONG Zikai ZHOU Zi Chao ZHANG junhai HAN Institute of Life Sciences the Key Laboratory of Developmental Genes and Human Disease Southeast University

Sleep is tightly governed by the circadian clock that contains a negative transcriptional feedback loop and synchronizes the physiology and behavior of most animals to daily environmental oscillations. In both vertebrates and invertebrates, the status of sleep and wake is controlled by the electrical activity of pacemaker neurons, which is circadian-regulated and suppressed by inhibitory GABAergic inputs. However, how the circadian clock rhythmically regulates the activity of pacemaker neuron is unclear. Here, we show that the level of Drosophila GABA receptor Resistant to Dieldrin(RDL) undergoes a daily cycle in wake-promoting large ventral lateral neurons(l-LNvs) and identify the E3 ligase Fbxl4 as a clock output molecule promoting RDL poly-ubiquitination and degradation. Depletion of Fbxl4 results in RDL accumulation, shortened sleep onset, and increased sleep time both in the day and the night. Moreover, we reveal that the expression of Fbxl4 in l-LNvs is Clock dependent but fbxl4 mutants exhibit normal locomotor rhythms. Thus, our study uncovers the critical molecular linkage between circadian clock and the electrical activity of pacemaker neurons and demonstrates that clock-dependent Fbxl4 expression downregulates GABAA receptor to increase the activity of pacemaker neurons and promote wakefulness.

关键词： Sleep circadian clock GABAA receptor E3 ligase Fbxl4 degradation

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Mutations of PQBP1 in Renpenning syndrome promote ubiquitin-mediated degradation of FMRP and cause synaptic dysfunction

Mutations of PQBP1 in Renpenning syndrome promote ubiquitin-...

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长三角地区神经科学论坛2017

作者： Xiao-Yan Zhang Junxia qi Yu-qian Shen Xian Liu An Liu Zikai Zhou junhai Han Zi Chao Zhang Institute of Life Sciences Southeast University

Renpenning syndrome is a group of X-linked intellectual disability syndromes caused by mutations in human polyglutamine-binding protein 1(PQBP1)*** is known about the molecular pathogenesis of the various mutations that cause the notable variability in *** this study,we examine the cellular and synaptic functions of the most com-mon mutations found in the patients:c.46162del AG,c.45962del AGAG and c.46364dup AG in an AG hexamer in PQBP1 exon *** discovered that PQBP1 c.45962del AGAG and c.46364dup AG mutations encode a new C-terminal epitope that preferentially binds non-phosphorylated fragile X mental retardation protein(FMRP)and promotes its ubiquitin-mediated *** of FMRP function up-regulates its targets such as MAP1B,and disrupts FMRP-dependent synaptic scaling in primary cultured *** Drosophila neuromuscular junction model,PQBP1 c.46364dup AG transgenic flies showed remarkable defects of synaptic over-growth,which can be rescued by exogenously expressing d *** data strongly support a gain-of-function pathogenic mechanism of PQBP1 c.45962del AGAG and c.46364dup AG mutations,and suggest that therapeutic strategies to restore FMRP function may be beneficial for those patients.

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基于MapReduce和Spark的大规模压缩模糊K-近邻算法

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计算机工程 2020年第11期46卷 139-147页

作者：王谟瀚翟俊海齐家兴河北大学数学与信息科学学院河北保定071002 河北大学河北省机器学习与计算智能重点实验室河北保定071002

压缩模糊K-近邻(CFKNN)算法仅适用于中小数据环境,且其样例选择采用静态机制,导致算法不能对阈值进行动态调整从而选出最优样例。为此,对CFKNN算法进行改进,将其扩展到大规模数据环境,提出分别基于MapReduce和Spark的2种大规模压缩模糊K... 详细信息

压缩模糊K-近邻(CFKNN)算法仅适用于中小数据环境,且其样例选择采用静态机制,导致算法不能对阈值进行动态调整从而选出最优样例。为此,对CFKNN算法进行改进,将其扩展到大规模数据环境,提出分别基于MapReduce和Spark的2种大规模压缩模糊K-近邻算法。在样例选择阈值设置方面,引入动态机制,使得所选样例更具代表性。在具有7个数据节点的大数据平台上进行实验,结果表明,与CFKNN算法相比,所提2种算法具有更高的分类精度和加速比。2个平台相比,MapReduce产生的中间文件数目多于Spark,而Spark在运行时间和同步次数上优于MapReduce。

关键词： MapReduce平台 Spark平台模糊K-近邻样例选择动态机制

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内配双圆钢管的钢骨混凝土短柱的轴压承载力

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工业建筑 2014年第7期44卷 151-154页

作者：王娟赵均海刘琦李艳长安大学建筑工程学院西安710061 信息产业部电子综合勘察研究院西安710054

基于双剪统一强度理论,分析了钢管以及处于三向受压的核心混凝土的受力状态,建立了内配双圆钢管的钢骨混凝土短柱的轴压极限承载力计算公式,并对影响因素进行了分析。将公式计算结果与相应文献试验结果对比,吻合良好;同时将该公式应用... 详细信息

基于双剪统一强度理论,分析了钢管以及处于三向受压的核心混凝土的受力状态,建立了内配双圆钢管的钢骨混凝土短柱的轴压极限承载力计算公式,并对影响因素进行了分析。将公式计算结果与相应文献试验结果对比,吻合良好;同时将该公式应用于工程实例,并将其计算结果、相应文献公式计算结果与有限元模拟结果进行对比后发现该公式计算结果吻合度较好。

关键词：统一强度理论三向受压双圆钢管极限承载力

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