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A new set of effective atomic charges of different conformers of alanine dipeptide is presented. These charges are obtained by fitting the electrostatic potential resulting from the ab initio SCF wave function of the system obtained in a 6-31G basis set. A specific fit procedure is used providing charges weakly dependent on the fit points as well as on the geometry of the molecule. It is shown that these charges retain a reasonable chemical meaning. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 473–482, 1999 相似文献
54.
Alternative difference analysis scheme combining R‐space EXAFS fit with global optimization XANES fit for X‐ray transient absorption spectroscopy 下载免费PDF全文
Time‐resolved X‐ray absorption spectroscopy (TR‐XAS), based on the laser‐pump/X‐ray‐probe method, is powerful in capturing the change of the geometrical and electronic structure of the absorbing atom upon excitation. TR‐XAS data analysis is generally performed on the laser‐on minus laser‐off difference spectrum. Here, a new analysis scheme is presented for the TR‐XAS difference fitting in both the extended X‐ray absorption fine‐structure (EXAFS) and the X‐ray absorption near‐edge structure (XANES) regions. R‐space EXAFS difference fitting could quickly provide the main quantitative structure change of the first shell. The XANES fitting part introduces a global non‐derivative optimization algorithm and optimizes the local structure change in a flexible way where both the core XAS calculation package and the search method in the fitting shell are changeable. The scheme was applied to the TR‐XAS difference analysis of Fe(phen)3 spin crossover complex and yielded reliable distance change and excitation population. 相似文献
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Xing L Kurumbail RG Frazier RB Davies MS Fujiwara H Weinberg RA Gierse JK Caspers N Carter JS McDonald JJ Moore WM Vazquez ML 《Journal of computer-aided molecular design》2009,23(1):13-24
Inducible, microsomal prostaglandin E synthase 1 (mPGES-1), the terminal enzyme in the prostaglandin (PG) biosynthetic pathway,
constitutes a promising therapeutic target for the development of new anti-inflammatory drugs. To elucidate structure–function
relationships and to enable structure-based design, an mPGES-1 homology model was developed using the three-dimensional structure
of the closest homologue of the MAPEG family (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism), mGST-1.
The ensuing model of mPGES-1 is a homo-trimer, with each monomer consisting of four membrane-spanning segments. Extensive
structure refinement revealed an inter-monomer salt bridge (K26-E77) as well as inter-helical interactions within each monomer,
including polar hydrogen bonds (e.g. T78-R110-T129) and hydrophobic π-stacking (F82-F103-F106), all contributing to the overall
stability of the homo-trimer of mPGES-1. Catalytic co-factor glutathione (GSH) was docked into the mPGES-1 model by flexible
optimization of both the ligand and the protein conformations, starting from the initial location ascertained from the mGST-1
structure. Possible binding site for the substrate, prostaglandin H2 (PGH2), was identified by systematically probing the refined molecular structure of mPGES-1. A binding model was generated by induced
fit docking of PGH2 in the presence of GSH. The homology model prescribes three potential inhibitor binding sites per mPGES-1 trimer. This was
further confirmed experimentally by equilibrium dialysis study which generated a binding stoichiometric ratio of approximately
three inhibitor molecules to three mPGES-1 monomers. The structural model that we have derived could serve as a useful tool
for structure-guided design of inhibitors for this emergently important therapeutic target. 相似文献
56.
含估计参数的加权经验过程 总被引:1,自引:0,他引:1
在讨论(广义)非参数似然比拟合优度检验时,加权经验过程理论是一个非常重要的基础.但对含估计参数的加权经验过程理论,目前文献中很少讨论.对含估计参数的加权经验过程的上界型和积分型两种统计量的近似分布进行了讨论,给出了较一般的结果.所得结论叮以为进一步讨论复合零假设下(广义)非参似然比拟合优度检验提供理论基础. 相似文献
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The Neighbor Cell Deposited Energy Ratio (NCDER) is a new method that is proposed to reconstruct incidence position in a single layer for a 3-dimensional imaging electromagnetic calorimeter (ECAL). This method was applied to reconstruct the ECAL test beam data for the Alpha Magnetic Spectrometer-02 (AMS-02). The results show that this method can achieve an angular resolution of 7.36±0.08°/√E+0.28±0.02° in the determination of the photon's direction, which is much more precise than that obtained with the commonly-adopted Center of Gravity (COG) method (8.4±0.1°/E+0.8±0.3°). Furthermore, since it uses only the properties of electromagnetic showers, this new method could also be used for other type of fine grain sampling calorimeters. 相似文献
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分析上海世博会在世博筹备建设和举办时期对上海市经济方面影响.筛选了世博会影响经济的四个方面(国民经济,财政收支,固定资产投资和对外经济贸易与旅游)的10个主要指标,构建了世博会影响经济的评价指标体系,针对每一项指标,利用1995年到2002的实际数据用指数回归拟合模型测算出2003-2010年在未筹办世博会情况下各项经济指标的估计(拟合)数据,并建立单指标的影响力指数模型,在分析2003年后的实际数据与拟合数据差异基础上,获得了上海世博会在每个指标方面对上海的影响力指数;建立了多指标综合影响力指数模型,得出总的经济影响力的指数为0.2403.考虑到2008年底金融危机势必会削弱世博会对经济的影响,通过参照另外两个同为中国直辖市的重庆和天津相同指标的变化,运用单独建立的模型,剔除金融危机对经济的影响,从而获得更客观地揭示世博对上海地区经济的真实影响程度.并就两个典型的指标给出了具体的演算过程,最后得到了消除了金融危机后的所有指标的影响力指数值,最终获得总的经济影响力的指数为0.2531,即世博会对上海市经济的实际贡献率为25.31%. 相似文献
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确定蛋白质-短肽复合物结构的新方法 总被引:1,自引:1,他引:0
大部分蛋白质 -蛋白质复合物的三维结构在接触表面都显示出很好的几何匹配 .由于蛋白质的表面几何形状和其它的一些物理化学性质在分子的专一性相互作用中起了主要作用 ,所以 ,接触表面几何形状的互补常常被认为是蛋白质分子识别的基础 .一般来说 ,蛋白质接触表面的几何匹配只涉及 5到 1 0几个紧密堆积的氨基酸残基 ,因此 ,蛋白质与蛋白质配体之间的识别计算可以通过蛋白质与突变周围的或与蛋白质表面紧密接触的配体肽段的识别计算来实现 . Stoddard等 [1] 已经利用从 MBP上选取的八肽成功地计算出接近晶体结构的 MBP-受体复合物 .许多研… 相似文献