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991.
Michael D. Reily Venkataraman Thanabal Michael E. Adams 《Journal of biomolecular NMR》1995,5(2):122-132
Summary The 48 amino acid peptides -Aga-IVA and -Aga-IVB are the first agents known to specifically block P-type calcium channels in mammalian brain, thus complementing the existing suite of pharmacological tools used for characterizing calcium channels. These peptides provide a new set of probes for studies aimed at elucidating the structural basis underlying the subtype specificity of calcium channel antagonists. We used 288 NMR-derived constraints in a protocol combining distance geometry and molecular dynamics employing the program DGII, followed by energy minimization with Discover to derive the three-dimensional structure of -Aga-IVB. The toxin consists of a well-defined core region, comprising seven solvent-shielded residues and a well-defined triple-stranded -sheet. Four loop regions have average backbone rms deviations between 0.38 and 1.31 Å, two of which are well-defined type-II -turns. Other structural features include disordered C- and N-termini and several conserved basic amino acids that are clustered on one face of the molecule. The reported structure suggests a possible surface for interaction with the channel. This surface contains amino acids that are identical to those of another known P-type calcium channel antagonist, -Aga-IVA, and is rich in basic residues that may have a role in binding to the anionic sites in the extracellular regions of the calcium channel.Abbreviations TOCSY
total correlated spectroscopy
- NOESY
nuclear Overhauser enhancement spectroscopy
- COSY
correlated spectroscopy 相似文献
992.
T. A. Kavanagh J. N. Timmis 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1986,72(3):337-345
Summary Restriction and hybridization analysis of cucumber native ribosomal (r) DNA purified from actinomycin-D/CsCl gradients suggested that the repeat units were heterogeneous in both length and sequence. Several full length rDNA repeat units were cloned and five are described which account for all the EcoR I and Xba I fragments present in native DNA. One of a number of BamH I sites found in the clones is not found in a proportion of native rDNA because of base modification. Restriction maps are described for the representative clones and aligned with R-loop maps obtained from electron microscope analysis of each type of repeat unit hybridized under R-loop conditions to pure 18S and 25S rRNAs. The major heterogeneity is explained by differences in length of the external spacer region and by a proportion of the repeat units showing a restriction fragment length polymorphism on EcoR I digestion. The regions coding for 18S and 25S rRNA are uninterrupted and highly conserved. 相似文献
993.
Four new complexes, {[Mn(imH)2(pdc)]·H2O}n (1), [Zn2(pdc)2(H2O)5]·2H2O (2), [Zn(imH)2(pdc)]·H2O (3), {[Zn2(pdc)2(bpy)(H2O)2]·5H2O}n (4) [imH = imidazole pdc = pyridine 2,6-dicarboxylate, bpy = 4,4′-bipyridine] have been synthesized under hydrothermal conditions and structurally characterized by elemental analysis, IR, PXRD, single-crystal X-ray diffraction and thermogravimetric analyses. All the four complexes display a three-dimensional (3D) open framework with one-dimensional (1D) channels that are filled with lattice water molecules. Particularly, in 4, the lattice water molecules form an infinite water chain. Both 1 and 4 consist of 1D polymeric chains. While 2 contains a dinuclear Zn(II) unit, and 3 is a mononuclear complex. Further, the result of thermal analysis of 1 and 2 shows the robustness of the overall supramolecular three-dimensional architecture. Complexes 1, 3, and 4 exhibit strong fluorescent emissions in the solid state at room temperature and could be significant in the field of photoactive materials. 相似文献
994.
Wang X Zhang C Chiang YC Toomey S Power MP Granoff ME Richardson R Xi W Lee DJ Chase S Laue TM Denis CL 《Protein science : a publication of the Protein Society》2012,21(9):1253-1268
A fundamental problem in proteomics is the identification of protein complexes and their components. We have used analytical ultracentrifugation with a fluorescence detection system (AU-FDS) to precisely and rapidly identify translation complexes in the yeast Saccharomyces cerevisiae. Following a one-step affinity purification of either poly(A)-binding protein (PAB1) or the large ribosomal subunit protein RPL25A in conjunction with GFP-tagged yeast proteins/RNAs, we have detected a 77S translation complex that contains the 80S ribosome, mRNA, and components of the closed-loop structure, eIF4E, eIF4G, and PAB1. This 77S structure, not readily observed previously, is consistent with the monosomal translation complex. The 77S complex abundance decreased with translational defects and following the stress of glucose deprivation that causes translational stoppage. By quantitating the abundance of the 77S complex in response to different stress conditions that block translation initiation, we observed that the stress of glucose deprivation affected translation initiation primarily by operating through a pathway involving the mRNA cap binding protein eIF4E whereas amino acid deprivation, as previously known, acted through the 43S complex. High salt conditions (1M KCl) and robust heat shock acted at other steps. The presumed sites of translational blockage caused by these stresses coincided with the types of stress granules, if any, which are subsequently formed. 相似文献
995.
Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 Å over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 Å over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures. 相似文献
996.
Alignments grow, secondary structure prediction improves. 总被引:12,自引:0,他引:12
Using information from sequence alignments significantly improves protein secondary structure prediction. Typically, more divergent profiles yield better predictions. Recently, various groups have shown that accuracy can be improved significantly by using PSI-BLAST profiles to develop new prediction methods. Here, we focused on the influences of various alignment strategies on two 8-year-old PHD methods. The following results stood out. (i) PHD using pairwise alignments predicts about 72% of all residues correctly in one of the three states: helix, strand, and other. Using larger databases and PSI-BLAST raised accuracy to 75%. (ii) More than 60% of the improvement originated from the growth of current sequence databases; about 20% resulted from detailed changes in the alignment procedure (substitution matrix, thresholds, and gap penalties). Another 20% of the improvement resulted from carefully using iterated PSI-BLAST searches. (iii) It is of interest that we failed to improve prediction accuracy further when attempting to refine the alignment by dynamic programming (MaxHom and ClustalW). (iv) Improvement through family growth appears to saturate at some point. However, most families have not reached this saturation. Hence, we anticipate that prediction accuracy will continue to rise with database growth. 相似文献
997.
Microarrays in ecology and evolution: a preview 总被引:23,自引:0,他引:23
Gibson G 《Molecular ecology》2002,11(1):17-24
998.
MATTHIEU FOLL MARTIN C. FISCHER GERALD HECKEL LAURENT EXCOFFIER 《Molecular ecology》2010,19(21):4638-4647
In the last decade, amplified fragment length polymorphisms (AFLPs) have become one of the most widely used molecular markers to study the genetic structure of natural populations. Most of the statistical methods available to study the genetic structure of populations using AFLPs consider these markers as dominant and are thus unable to distinguish between individuals being heterozygous or homozygous for the dominant allele. Some attempts have been made to treat AFLPs as codominant markers by using AFLP band intensities to infer the most likely genotype of each individual. These two approaches have some drawbacks, the former discarding potentially valuable information and the latter being sometimes unable to correctly assign genotypes to individuals. In this study, we propose an alternative likelihood‐based approach, which does not attempt at inferring the genotype of each individual, but rather incorporate the uncertainty about genotypes into a Bayesian framework leading to the estimation of population‐specific FIS and FST coefficients. We show with simulations that the accuracy of our method is much higher than one using AFLP as dominant markers and is generally close to what would be obtained by using the same number of Single‐Nucleotide Polymorphism (SNP) markers. The method is applied to a data set of four populations of the common vole (Microtus arvalis) from Grisons in Switzerland, for which we obtained 562 polymorphic AFLP markers. Our approach is very general and has the potential to make AFLP markers as useful as SNP data for nonmodel species. 相似文献
999.
Christina Bremer Gesche Braker Diethart Matthies Carl Beierkuhnlein & Ralf Conrad 《FEMS microbiology ecology》2009,70(3):45-55
To explore potential links between plant communities, soil denitrifiers and denitrifier function, the impact of presence, diversity (i.e. species richness) and plant combination on nirK -type denitrifier community composition and on denitrifier activity was studied in artificial grassland plant assemblages over two consecutive years. Mesocosms containing zero, four and eight species and different combinations of two species were set up. Differences in denitrifier community composition were analysed by canonical correspondence analyses following terminal restriction fragment length polymorphism analysis of PCR-amplified nirK gene fragments coding for the copper-containing nitrite reductase. As a measure of denitrifier function, denitrifier enzyme activity (DEA) was determined in the soil samples. The presence as well as the combination of plants and sampling time, but not plant diversity, affected the composition of the nirK -type denitrifier community and DEA. Denitrifier activity significantly increased in the presence of plants, especially when they were growing during summer and autumn. Overall, we found a strong and direct linkage of denitrifier community composition and functioning, but also that plants had additional effects on denitrifier function that could not be solely explained by their effects on nirK -type denitrifier community composition. 相似文献
1000.
Rajesh Nair Jinfeng Liu Ta-Tsen Soong Thomas B. Acton John K. Everett Andrei Kouranov Andras Fiser Adam Godzik Lukasz Jaroszewski Christine Orengo Gaetano T. Montelione Burkhard Rost 《Journal of structural and functional genomics》2009,10(2):181-191
The Protein Structural Initiative (PSI) at the US National Institutes of Health (NIH) is funding four large-scale centers
for structural genomics (SG). These centers systematically target many large families without structural coverage, as well
as very large families with inadequate structural coverage. Here, we report a few simple metrics that demonstrate how successfully
these efforts optimize structural coverage: while the PSI-2 (2005-now) contributed more than 8% of all structures deposited
into the PDB, it contributed over 20% of all novel structures (i.e. structures for protein sequences with no structural representative
in the PDB on the date of deposition). The structural coverage of the protein universe represented by today’s UniProt (v12.8)
has increased linearly from 1992 to 2008; structural genomics has contributed significantly to the maintenance of this growth
rate. Success in increasing novel leverage (defined in Liu et al. in Nat Biotechnol 25:849–851, 2007) has resulted from systematic
targeting of large families. PSI’s per structure contribution to novel leverage was over 4-fold higher than that for non-PSI
structural biology efforts during the past 8 years. If the success of the PSI continues, it may just take another ~15 years
to cover most sequences in the current UniProt database. 相似文献