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Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution. 总被引:5,自引:1,他引:4 下载免费PDF全文
A. E. Eriksson L. S. Cousens B. W. Matthews 《Protein science : a publication of the Protein Society》1993,2(8):1274-1284
The three-dimensional structure of human basic fibroblast growth factor has been refined to a crystallographic residual of 16.1% at 1.6 A resolution. The structure has a Kunitz-type fold and is composed of 12 antiparallel beta-strands, 6 of which form a beta-barrel. One bound sulfate ion has been identified in the model, hydrogen bonded to the side chains of Asn 27, Arg 120, and Lys 125. The side chain of Arg 120 has two conformations, both of which permit hydrogen bonds to the sulfate. This sulfate binding site has been suggested as the binding site for heparin (Eriksson, A.E., Cousens, L.S., Weaver, L.H., & Matthews, B.W., 1991, Proc. Natl. Acad. Sci. USA 88, 3441-3445). Two beta-mercaptoethanol (BME) molecules are also included in the model, each forming a disulfide bond to the S gamma atoms of Cys 69 and Cys 92, respectively. The side chain of Cys 92 has two conformations of which only one can bind BME. Therefore the BME molecule is half occupied at this site. The locations of possible sulfate binding sites on the protein were examined by replacing the ammonium sulfate in the crystallization medium with ammonium selenate. Diffraction data were measured to 2.2 A resolution and the structure refined to an R-factor of 13.8%. The binding of the more electron-dense selenate ion was identified at two positions. One position was identical to the sulfate binding site identified previously. The second selenate binding site, which is of lower occupancy, is situated 5.6 A from the first. This ion is hydrogen bonded by the side chain of Lys 135 and Arg 120. Thus the side chain of Arg 120 binds two selenate ions simultaneously. It is suggested that the observed second selenate binding site should also be considered as a possible binding site for heparin, or that both selenate binding sites might simultaneously contribute to the binding of heparin. 相似文献
104.
New tricks of an old pattern: structural versatility of scorpion toxins with common cysteine spacing
Saucedo AL Flores-Solis D Rodríguez de la Vega RC Ramírez-Cordero B Hernández-López R Cano-Sánchez P Noriega Navarro R García-Valdés J Coronas-Valderrama F de Roodt A Brieba LG Domingos Possani L del Río-Portilla F 《The Journal of biological chemistry》2012,287(15):12321-12330
Scorpion venoms are a rich source of K(+) channel-blocking peptides. For the most part, they are structurally related small disulfide-rich proteins containing a conserved pattern of six cysteines that is assumed to dictate their common three-dimensional folding. In the conventional pattern, two disulfide bridges connect an α-helical segment to the C-terminal strand of a double- or triple-stranded β-sheet, conforming a cystine-stabilized α/β scaffold (CSα/β). Here we show that two K(+) channel-blocking peptides from Tityus scorpions conserve the cysteine spacing of common scorpion venom peptides but display an unconventional disulfide pattern, accompanied by a complete rearrangement of the secondary structure topology into a CS helix-loop-helix fold. Sequence and structural comparisons of the peptides adopting this novel fold suggest that it would be a new elaboration of the widespread CSα/β scaffold, thus revealing an unexpected structural versatility of these small disulfide-rich proteins. Acknowledgment of such versatility is important to understand how venom structural complexity emerged on a limited number of molecular scaffolds. 相似文献
105.
Athavale SS Gossett JJ Hsiao C Bowman JC O'Neill E Hershkovitz E Preeprem T Hud NV Wartell RM Harvey SC Williams LD 《RNA (New York, N.Y.)》2012,18(4):752-758
The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution. 相似文献
106.
Bacterial lipoproteins play an important role in bacterial pathogenesis and physiology. The genome of Campylobacter jejuni, a major foodborn pathogen, is predicted to contain over 20 lipoproteins. However, the functions of the majority of C. jejuni lipoproteins remain unknown. The Cj0090 protein is encoded by a lipoprotein operon composed of cj0089, cj0090, and cj0091. Here, we report the crystal structure of Cj0090 at 1.9 Å resolution, revealing a novel variant of the immunoglobulin fold with β‐sandwich architecture. The structure suggests that Cj0090 may be involved in protein‐protein interactions, consistent with a possible role for bacterial lipoproteins. Proteins 2012;. © 2012 Wiley Periodicals, Inc. 相似文献
107.
Human phonation does not merely depend on the vibration of the vocal folds. Research by clinical and computer simulations has demonstrated that the false vocal fold (FVF) is an important laryngeal con-striction that plays a vital role during human voice production. This study explored the effects of the FVF gaps using both the three-dimensional Plexiglas model and the numerical computation methods. Twelve FVF gaps (ranging from 0.02 to 2.06 cm) were used in this study at three glottal angles (uniform and convergent/divergent 40°), two minimal glottal diameters (Dg) (0.04 cm and 0.06 cm) separately, and the constant subglottal pressure (8 cm H2O). The results suggested that (1) the intralaryngeal pressure was the lowest and the flow was the highest (least flow resistance) when the FVF gap was 1.5-2 times greater than Dg; (2) the divergent glottal angle gave lower pressure and greater flow than the conver-gent and uniform glottal angle as there were no FVF conditions; (3) the presence of the FVF decreased the effects of the glottal angle to a certain extent; and more importantly, (4) the presence of the FVF also moved the separation points downstream, straightened the glottal jet for a longer distance, decreased the overall laryngeal resistance, and reduced the energy dissipation, suggesting the significance of FVF in efficient voice production. These results may be incorporated in the phonatory models (physical or computational) for better understanding of vocal mechanics. The results might also be helpful in exploring the surgical and rehabilitative intervention of related voice problems. 相似文献
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Georgios N. Hatzopoulos 《FEBS letters》2010,584(5):1011-1015
The crystal structure of the free form of IF1 from Mycobacterium tuberculosis has been determined at 1.47 Å resolution. The structure adopts the expected OB fold and matches the high structural conservation among IF1 orthologues. In order to further explore the function of Mtb-IF1, we built a model of its interaction with the 30S ribosomal subunit based on the crystal structure of the complex from Thermus thermophilus. The model suggests that several functionally important side chain residues undergo large movements while the rest of the protein in complex shows only very limited conformational change as compared to its form in solution. 相似文献
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