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1.
Jonathan D. Nickels Joseph E. Curtis Hugh O’Neill Alexei P. Sokolov 《Journal of biological physics》2012,38(3):497-505
Recent studies have discovered strong differences between the dynamics of nucleic acids (RNA and DNA) and proteins, especially at low hydration and low temperatures. This difference is caused primarily by dynamics of methyl groups that are abundant in proteins, but are absent or very rare in RNA and DNA. In this paper, we present a hypothesis regarding the role of methyl groups as intrinsic plasticizers in proteins and their evolutionary selection to facilitate protein dynamics and activity. We demonstrate the profound effect methyl groups have on protein dynamics relative to nucleic acid dynamics, and note the apparent correlation of methyl group content in protein classes and their need for molecular flexibility. Moreover, we note the fastest methyl groups of some enzymes appear around dynamical centers such as hinges or active sites. Methyl groups are also of tremendous importance from a hydrophobicity/folding/entropy perspective. These significant roles, however, complement our hypothesis rather than preclude the recognition of methyl groups in the dynamics and evolution of biomolecules. 相似文献
2.
G. N. Borisyuk R. M. Borisyuk A. B. Kirillov E. I. Kovalenko V. I. Kryukov 《Biological cybernetics》1985,52(5):301-306
A new method is proposed to analyse dependencies in point processes, which takes into account specific character of neuronal activity. Simulation modelling of neuronal network revealed that the estimated weight of connection depends monotonically on the value of the model synaptic strength. In contrast to the crosscorrelation, the method allows for nonlinear interconnections and does not require point processes to be stationary and samples to be large. Examples are presented of the method's application to neurophysiological data analysis. 相似文献
3.
G. P. Polovinko O. N. Yaroslavtseva Z. A. Teshebaeva V. Yu. Kryukov 《Contemporary Problems of Ecology》2010,3(5):515-521
The paper studies mycobiota of the dead insects in West Siberia, Primorsky krai, and Kyrgyzstan. Ascomycetes anamorphs of
13 genera are revealed. In all regions Beauveria bassiana (Bals.-Criv.) Vuill. dominated comprising on average 68% of the total number of isolates. The fungus hosts list the insects
of 7 orders and 32 families with Coleoptera, Lepidoptera, and Hemiptera dominating. The rarely found entomopathogens include
Tolypocladium inflatum Gams (primarily on Lepidoptera), Metarhizium anisopliae (Metschn.) Sorokin (on Coleoptera). The mortality rate of the insects due to micromycetes is observed mainly on enzootic
level. The study of the pathogenic properties of the dominating species (B. bassiana) show the absence of specificity of its environmental isolates for a number of representatives of Orthoptera, Lepidoptera,
Coleoptera, and Diptera. 相似文献
4.
Daisuke Hirata Alexei V. Abramov Gennady F. Baryshnikov Ryuichi Masuda 《Biological journal of the Linnean Society. Linnean Society of London》2014,111(3):627-635
Sequence analyses of the complete brown bear, Ursus arctos, mitochondrial DNA (mtDNA) genome have detected scattered single nucleotide polymorphisms (SNPs) that define distinct mtDNA haplogroups in phylogeographical studies. The degraded DNA in historical samples, such as stuffed or excavated specimens, however, is often not suitable for sequence analyses. To address this problem, we developed an amplified product length polymorphism (APLP) analysis for mtDNA‐haplogrouping U. arctos specimens by detecting haplogroup‐specific SNPs. We verified the validity and utility of this method by analysing up to 170‐year‐old skin samples from U. arctos specimens collected widely across continental Eurasia. We detected some of the same haplogroups as those occurring in eastern Hokkaido (Japan) and eastern Alaska in continental Eurasia (the Altai and the Caucasus). Our results show that U. arctos in eastern Hokkaido and eastern Alaska descended from a common ancestor in continental Eurasia, and suggest that U. arctos occupied several refugia in southern Asia during the Last Glacial Maximum. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 627–635. 相似文献
5.
The nucleotide sequence of the BalI-PstI fragment of T5 DNA, 1347 bp in length, coding for 5'-exonuclease (D15 gene), has been determined. A coding region of the gene contains 873 bp and is preceded by a typical Shine-Dalgarno sequence. The D15 gene belongs to a cluster, consisting of at least 3 genes, in which a termination codon of a preceding gene overlaps an initiation codon of the following one. The sequence contains an open reading frame for 291 amino acid residues. The molecular mass of the 5'-exonuclease calculated from the predicted amino acid sequence is 33 400 Da. 相似文献
6.
Cloning of bacteriophage T5 promoters 总被引:3,自引:0,他引:3
Vladimir N. Ksenzenko Tatjana P. Kamynina Nina M. Pustoshilova Valentine M. Kryukov A. A. Bayev 《Molecular & general genetics : MGG》1982,185(3):520-522
Summary Bacteriophage T5 was subjected to combined hydrolysis with the restriction endonuclease PstI and HindIII and the resulting fragments were inserted into the plasmid pBR322. Selection of transformants for Aps-Tcr-phenotype made it possible to screen the hybrid plasmids that contained promoter sequences in the cloned fragments.Two PstI/HindIII fragment, 720 bp (51% of the T5 DNA length) and 1,200 bp (70%) were cloned in this study. Tcr levels for these plasmids were as high as 18 g/ml and 75 g/ml, respectively. The presence of Escherichia coli RNA polymerase binding sites on both fragments was shown using the nitrocellulose filter assay. These binding sites are situated between 35 bp and 95 bp from the HindIII cleavage site on the 1,200 bp fragment; and within 420 bp from the HindIII site on the 720 bp fragment.Abbreviations Ap
ampicillin
- Tc
tetracycline
- bp
base pairs
- NTPs
nucleoside triphosphates
- PBB
polymerase binding buffer 相似文献
7.
Nikulin A Eliseikina I Tishchenko S Nevskaya N Davydova N Platonova O Piendl W Selmer M Liljas A Drygin D Zimmermann R Garber M Nikonov S 《Nature structural biology》2003,10(2):104-108
The L1 protuberance of the 50S ribosomal subunit is implicated in the release/disposal of deacylated tRNA from the E site. The apparent mobility of this ribosomal region has thus far prevented an accurate determination of its three-dimensional structure within either the 50S subunit or the 70S ribosome. Here we report the crystal structure at 2.65 A resolution of ribosomal protein L1 from Sulfolobus acidocaldarius in complex with a specific 55-nucleotide fragment of 23S rRNA from Thermus thermophilus. This structure fills a major gap in current models of the 50S ribosomal subunit. The conformations of L1 and of the rRNA fragment differ dramatically from those within the crystallographic model of the T. thermophilus 70S ribosome. Incorporation of the L1-rRNA complex into the structural models of the T. thermophilus 70S ribosome and the Deinococcus radiodurans 50S subunit gives a reliable representation of most of the L1 protuberance within the ribosome. 相似文献
8.
V. I. Kryukov 《Cognitive neurodynamics》2012,6(5):377-398
There are three basic paradigms of classical conditioning: delay, trace and context conditioning where presentation of a conditioned stimulus (CS) or a context typically predicts an unconditioned stimulus (US). In delay conditioning CS and US normally coterminate, whereas in trace conditioning an interval of time exists between CS termination and US onset. The modeling of trace conditioning is a rather difficult computational problem and is a challenge to the behavior and connectionist approaches mainly due to a time gap between CS and US. To account for trace conditioning, Pavlov (Conditioned reflexes: an investigation of the physiological activity of the cerebral cortex, Oxford University Press, London, 1927) postulated the existence of a stimulus “trace” in the nervous system. Meanwhile, there exist many other options for solving this association problem. There are several excellent reviews of computational models of classical conditioning but none has thus far been devoted to trace conditioning. Eight representative models of trace conditioning aimed at building a prospective model are being reviewed below in a brief form. As a result, one of them, comprising the most important features of its predecessors, can be suggested as a real candidate for a unified model of trace conditioning. 相似文献
9.
Babu M Beloglazova N Flick R Graham C Skarina T Nocek B Gagarinova A Pogoutse O Brown G Binkowski A Phanse S Joachimiak A Koonin EV Savchenko A Emili A Greenblatt J Edwards AM Yakunin AF 《Molecular microbiology》2011,79(2):484-502
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show that the purified Cas1 protein of Escherichia coli (YgbT) exhibits nuclease activity against single-stranded and branched DNAs including Holliday junctions, replication forks and 5'-flaps. The crystal structure of YgbT and site-directed mutagenesis have revealed the potential active site. Genome-wide screens show that YgbT physically and genetically interacts with key components of DNA repair systems, including recB, recC and ruvB. Consistent with these findings, the ygbT deletion strain showed increased sensitivity to DNA damage and impaired chromosomal segregation. Similar phenotypes were observed in strains with deletion of CRISPR clusters, suggesting that the function of YgbT in repair involves interaction with the CRISPRs. These results show that YgbT belongs to a novel, structurally distinct family of nucleases acting on branched DNAs and suggest that, in addition to antiviral immunity, at least some components of the CRISPR-Cas system have a function in DNA repair. 相似文献
10.
Aerobic glycolysis is a seemingly wasteful mode of ATP production that is seen both in rapidly proliferating mammalian cells and highly active contracting muscles, but whether there is a common origin for its presence in these widely different systems is unknown. To study this issue, here we develop a model of human central metabolism that incorporates a solvent capacity constraint of metabolic enzymes and mitochondria, accounting for their occupied volume densities, while assuming glucose and/or fatty acid utilization. The model demonstrates that activation of aerobic glycolysis is favored above a threshold metabolic rate in both rapidly proliferating cells and heavily contracting muscles, because it provides higher ATP yield per volume density than mitochondrial oxidative phosphorylation. In the case of muscle physiology, the model also predicts that before the lactate switch, fatty acid oxidation increases, reaches a maximum, and then decreases to zero with concomitant increase in glucose utilization, in agreement with the empirical evidence. These results are further corroborated by a larger scale model, including biosynthesis of major cell biomass components. The larger scale model also predicts that in proliferating cells the lactate switch is accompanied by activation of glutaminolysis, another distinctive feature of the Warburg effect. In conclusion, intracellular molecular crowding is a fundamental constraint for cell metabolism in both rapidly proliferating- and non-proliferating cells with high metabolic demand. Addition of this constraint to metabolic flux balance models can explain several observations of mammalian cell metabolism under steady state conditions. 相似文献