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131.
Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein–ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl‐xL complex with ABT‐737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single‐ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X‐ray crystallographic maps, and aiding fragment‐based drug design, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 相似文献
132.
Dmitry V. Peryshkov 《Journal of fluorine chemistry》2010,131(11):1252-1256
The anhydrous salt K2B12F12 crystallized from aqueous solution and its structure was determined by single crystal X-ray diffraction. The Ni2In-type structure it exhibits is rare for an A2X ionic compound at 25 °C and 1 atm., consisting of an expanded hexagonal close-packed array of B12F122− centroids (cent?cent distances: 7.204-8.236 Å) with half of the K+ ions filling all of the Oh holes and half of the K+ ions filling all of the D3h trigonal holes in the close-packed layers that are midway between two “empty” Td holes. The structure is also unusual in that the bond-valence sum for the K+ ions in Oh holes is less than or equal to 0.73 (the bond-valence sum for the other type of K+ ion is 1.16). A variation of the Ni2In structure is exhibited by the previously published monohydrate Cs2(H2O)B12F12, for which an improved structure is also reported here. For K2B12F12: monoclinic, C2/c, a = 8.2072(8), b = 14.2818(7), c = 11.3441(9) Å, β = 92.832(5)°, Z = 4, T = 120(2) K. For Cs2(H2O)B12F12: orthorhombic, P212121, a = 9.7475(4), b = 10.2579(4), c = 15.0549(5) Å, Z = 4, T = 110(1) K. 相似文献
133.
Biological specimens have to be prepared for imaging in the electron microscope in a way that preserves their native structure. Two-dimensional (2D) protein crystals to be analyzed by electron crystallography are best preserved by sugar embedding. One of the sugars often used to embed 2D crystals is trehalose, a disaccharide used by many organisms for protection against stress conditions. Sugars such as trehalose can also be added to negative staining solutions used to prepare proteins and macromolecular complexes for structural studies by single-particle electron microscopy (EM). In this review, we describe trehalose and its characteristics that make it so well suited for preparation of EM specimens and we review specimen preparation methods with a focus on the use of trehalose. 相似文献
134.
Jia‐Jian Wang Hua‐Ming Zeng Zhi‐Gang She Cheng‐Du Miao Kui Hong Yu‐Cheng Gu Lan Liu Yong‐Cheng Lin 《Helvetica chimica acta》2011,94(10):1875-1880
Two new meroterpenes, ‘acetoxydehydroaustin B’ ( 1 ) and ‘1,2‐dihydro‐acetoxydehydroaustin B’ ( 2 ) were isolated in the form of a mixed crystal from the mangrove endophytic fungus Aspergillus sp. 085241B. Their structures and absolute configurations were determined by extensive analysis of their spectra and X‐ray diffraction data. In a preliminary bioassay, the mixed crystal did not exhibit activities against cancer cell lines of MDA‐MB‐435, SKBR3, HepG2, HEP3B, PC‐3, and A549, as well as against α‐glucosidase and tyrosinase. 相似文献
135.
Planarly chiral ferrocene derivatives with bridged cyclopentadienyl rings are interesting ligands in asymmetric catalysis. A planar stereogenic unit is conveniently introduced by diastereoselective ortho-lithiation. The directed lithiation of several [5]ferrocenophane derivatives followed by quenching with chlorodiphenylphosphane led to planarly chiral ligands. The sense of diastereoselection was studied by computational methods. Absolute configuration of methoxy phosphane was determined by single crystal X-ray diffraction study. 相似文献
136.
Cristian Bodin Fredrik Mauritzson Rob Horsefield Anna Aagaard Hongwei Guo Linda Öster Lisa Wissler Margareta Ek 《Journal of synchrotron radiation》2012,19(2):288-289
Currently there is no rack system for the long‐term storage of SPINE pucks in spite of their commercial availability and heavy usage at the ESRF. The only way to store pucks is in transport dewar canisters which presents a number of limitations and drawbacks. Here a simple affordable rack for storing SPINE pucks is described, which we believe is accessible to not only synchrotrons but also both academic and industrial research laboratories. 相似文献
137.
Du‐Qiang Luo Wen‐Liang Zhu Xiao‐Long Yang Shu‐Juan Liang Zhi‐Ran Cao 《Helvetica chimica acta》2010,93(6):1209-1215
Two new daphniphyllum alkaloids named 2‐hydroxyyunnandaphnine D ( 1 ) and methyl 7‐hydroxyhomodaphniphyllate ( 2 ), together with eight known alkaloids, daphnioldhanin D, calyciphylline F, calyciphylline B, deoxycalyciphylline B, daphnicyclidin H, macropodumine C, 9,10‐epoxycalycine A, and yunnandaphnine A, were isolated from the stems and leaves of Daphniphyllum calycinum. Their structures and relative configurations were established on the basis of spectral evidence (including 2D‐NMR) and subsequently confirmed by a single‐crystal X‐ray crystallographic diffraction analysis. 相似文献
138.
Lorien J. Parker Louis C. Italiano Craig J. Morton Nancy C. Hancock David B. Ascher Jade B. Aitken Hugh H. Harris Pablo Campomanes Ursula Rothlisberger Anastasia De Luca Mario Lo Bello Wee Han Ang Paul J. Dyson Michael W. Parker 《Chemistry (Weinheim an der Bergstrasse, Germany)》2011,17(28):7705-7705
139.
Rachid Touzani Michael HaibachAgnieszka J. Nawara-Hultzsch Sghir El KadiriThomas J. Emge Alan S. Goldman 《Polyhedron》2011,30(15):2530-2534
The complexation of the simple 1-hydroxymethyl-3,5-dimethylpyrazole (HL) ligand with Fe and Ni salts leads to interesting polynuclear complexes in good yield. X-ray diffraction reveals that the resulting complexes (μ4-L)4Ni4Cl4(H2O)4 and (μ2-L)4(μ3-L)2Fe8Cl16(μ4-O)6 adopt cubane-type and open-cubane-type structures in the solid state. 相似文献
140.
报道了4-甲氧基.2-溴代丁烯内酯(4)与几种醇通过串联的双。Michael加成及分子内的亲核取代反应,简便地得到了环丙烷类化合物8。经元素分析、IR、^1HNMR、^13CNMR和MS对目标产物进行了结构表征,其中8a通过单晶培养和x射线晶体测定,确定了它的立体结构。 相似文献