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Christopher J. R. Illingworth Paul D. Scott Kevin E. B. Parkes Christopher R. Snell Matthew P. Campbell Christopher A. Reynolds 《Journal of computational chemistry》2010,31(15):2677-2688
Here, we describe a family of methods based on residue–residue connectivity for characterizing binding sites and apply variants of the method to various types of protein–ligand complexes including proteases, allosteric‐binding sites, correctly and incorrectly docked poses, and inhibitors of protein–protein interactions. Residues within ligand‐binding sites have about 25% more contact neighbors than surface residues in general; high‐connectivity residues are found in contact with the ligand in 84% of all complexes studied. In addition, a k‐means algorithm was developed that may be useful for identifying potential binding sites with no obvious geometric or connectivity features. The analysis was primarily carried out on 61 protein–ligand structures from the MEROPS protease database, 250 protein–ligand structures from the PDBSelect (25%), and 30 protein–protein complexes. Analysis of four proteases with crystal structures for multiple bound ligands has shown that residues with high connectivity tend to have less variable side‐chain conformation. The relevance to drug design is discussed in terms of identifying allosteric‐binding sites, distinguishing between alternative docked poses and designing protein interface inhibitors. Taken together, this data indicate that residue–residue connectivity is highly relevant to medicinal chemistry. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 相似文献
775.
<正>In this work,the formation sites,helical parameters and hydrogen bond positions of Konjac glucomannan molecular helices were investigated using molecular dynamic simulation method.To our interest,the KGM chain is mainly composed by local left and right helix structures. The formation sites of KGM chain might locate at the chain-segments containing acetyl groups,and the left helix is the favorable conformation of KGM.Temperature-dependent molecule conformation study indicates that the right helix is dominant when the temperature is lower than 343 K,above which,however,the left helix is dominating(right helix disappears).In addition,intramolecular hydrogen bonds in the left helix can be found at the-OH groups on C(2),C(4)and C(6)of mannose residues;comparably,the intramolecular hydrogen bonds in the right helix can be mainly observed at the-OH groups on C(4)and C(6)of the mannose residues and C(3)of the glucose residues.In conclusion,molecular dynamic simulation is an efficient method for the microscopic conformation study of glucomannan molecular helices. 相似文献
776.
Viviana P. Ramunni Carolina Hurtado-Noreña Pablo Bruzzoni 《Physica B: Condensed Matter》2012,407(16):3301-3304
We calculate the equilibrium energies and migration barriers of Fe, Cr and H interstitial defects in α-FeX(X=Cr). We use the ab-initio electronic structure code, SIESTA, coupled to the monomer method to find activated states (or migration barriers), in order to study atomic defects diffusion. Ab-initio calculations reveal that in the presence of Cr the H migration barriers are higher than in pure α-Fe. On the other hand, our permeation tests on 9%Cr–91%Fe alloys reveal a permeation coefficient 10 times lower and a diffusion coefficient 200 times lower than in pure, annealed iron. Focusing on our experimental results, we explore very simple model of new H trapping sites and possible migration paths that can explain the experimental observations. 相似文献
777.
Mohamed I. Zaki Muhammad A. Hasan Fakhryia A. Al-Sagheer Lata Pasupulety 《Colloids and surfaces. A, Physicochemical and engineering aspects》2001,190(3):710-274
Exposure of strong Lewis (coordinatively unsaturated metal atoms) and Bronsted (proton donor OH-groups) acid sites on solid surfaces is a prime demand for potential adsorptive and catalytic applications. In situ FTIR spectroscopy of small adsorbed base molecules, often NH3, pyridine, CH3CN, NO or CO molecules, has been well established as a powerful surface analytical technique for characterization of nature, strength and concentration of acid sites. Pyridine (Py) has been preferred as an IR probe molecule of finely divided metal oxide surfaces at room (RT) and higher temperature regimes, since it is (i) more selective and stable than NH3; (ii) much more strongly adsorbed than CO and CH3CN; and (iii) relatively more sensitive to the strength of Lewis acid sites than NO. In the present work, in situ IR spectra of Py adsorbed at ≥RT on characterized alumina, silica, silica–alumina, titania, zirconia and ceria were measured, and compared with RT-spectra of liquid and gas phase Py obtained under identical spectroscopic conditions, in order to characterize spectral consequences of mutual Py–Py interactions in the adsorbed phase. It has been concluded that the availability of Lewis acid sites can be unequivocally monitored by formation of coordinated Py molecules giving rise to IR-absorption(s) due to the ν8a mode of νCCN vibrations at 1630–1600 cm−1, where the higher the frequency assumed, the stronger the acidity of the site. Formation of pyridinium surface species (PyH+) is identifiable by (i) an ν8a-absorption at ≥1630 cm−1; (ii) an ν19b-absorption at 1550–1530 cm−1; as well as (iii) νN+---H and δN+---H absorptions occurring, respectively, near 2450 and 1580 cm−1, and, thus, the availability of Bronsted acid sites. Moreover, products and IR-characteristics of Py surface reactions at >RT have been identified, and used to imply nature of surface base sites (OH−and O2−) involved in formation of acid–base site pairs. 相似文献
778.
S. Yamanaka D. Yamaki Y. Shigeta H. Nagao K. Yamaguchi 《International journal of quantum chemistry》2001,84(6):670-676
We have implemented ab initio linear combinations of Gaussian‐type orbital calculations with generalized localized spin density approximation (GLSDA) for a dimer of equilateral H3 as a model of the noncollinear magnetic clusters. It has been found that the GLSDA solution with the three‐dimensional noncollinear spin structure is, contrary to prior band calculations by other groups, the ground state near the Oh conformation. Further computational results are compared to that of ab initio generalized Hartree–Fock. The difference between them and the influence of the correlation correction were discussed. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 相似文献
779.
Antal Tungler 《Reaction Kinetics and Catalysis Letters》2001,74(2):271-276
On the basis of reviewed works and our experiences we propose that during the reduction of the surface the adsorbing substrates and the chiralcompounds induce the formation of chiral surface sites in dia- or enantioselective hydrogenation reactions catalyzed by precious metal 相似文献
780.
液相色谱/电喷雾质谱(LC/ESI/MS)在蛋白质分析鉴定中的应用 总被引:2,自引:0,他引:2
对液相色谱/电喷雾质谱(LC/ESI/MS)在蛋白质分子量测定、一级结构的分析、蛋白质和多肽纯度的鉴定、肽质量酶谱、蛋白质分子内二硫键的定量和定位、磷酰化位置的测定以及在蛋白质组中的应用等方面进行了综述和讨论。 相似文献