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941.
Yonglan Liu Mingzhen Zhang Hyunbum Jang Ruth Nussinov 《Protein science : a publication of the Protein Society》2023,32(1):e4504
Bcr-Abl, a nonreceptor tyrosine kinase, is associated with leukemias, especially chronic myeloid leukemia (CML). Deletion of Abl's N-terminal region, to which myristoyl is linked, renders the Bcr-Abl fusion oncoprotein constitutively active. The substitution of Abl's N-terminal region by Bcr enables Bcr-Abl oligomerization. Oligomerization is critical: it promotes clustering on the membrane, which is essential for potent MAPK signaling and cell proliferation. Here we decipher the Bcr-Abl specific, step-by-step oligomerization process, identify a specific packing surface, determine exactly how the process is structured and identify its key elements. Bcr's coiled coil (CC) domain at the N-terminal controls Bcr-Abl oligomerization. Crystallography validated oligomerization via Bcr-Abl dimerization between two Bcr CC domains, with tetramerization via tight packing between two binary assemblies. However, the structural principles guiding Bcr CC domain oligomerization are unknown, hindering mechanistic understanding and drugs exploiting it. Using molecular dynamics (MD) simulations, we determine that the binary complex of the Bcr CC domain serves as a basic unit in the quaternary complex providing a specific surface for dimer–dimer packing and higher-order oligomerization. We discover that the small α1-helix is the key. In the binary assembly, the helix forms interchain aromatic dimeric packing, and in the quaternary assembly, it contributes to the specific dimer–dimer packing. Our mechanism is supported by the experimental literature. It offers the key elements controlling this process which can expand the drug discovery strategy, including by Bcr CC-derived peptides, and candidate residues for small covalent drugs, toward quenching oligomerization, supplementing competitive and allosteric tyrosine kinase inhibitors. 相似文献
942.
Gopinath Chattopadhyay Shahbaz Ahmed Nonavinakere Seetharam Srilatha Aparna Asok Raghavan Varadarajan 《Protein science : a publication of the Protein Society》2023,32(1):e4514
Regulation of biological processes by proteins often involves the formation of transient, multimeric complexes whose characterization is mechanistically important but challenging. The bacterial toxin CcdB binds and poisons DNA Gyrase. The corresponding antitoxin CcdA extracts CcdB from its complex with Gyrase through the formation of a transient ternary complex, thus rejuvenating Gyrase. We describe a high throughput methodology called Ter-Seq to stabilize probable ternary complexes and measure associated kinetics using the CcdA-CcdB-GyrA14 ternary complex as a model system. The method involves screening a yeast surface display (YSD) saturation mutagenesis library of one partner (CcdB) for mutants that show enhanced ternary complex formation. We also isolated CcdB mutants that were either resistant or sensitive to rejuvenation, and used surface plasmon resonance (SPR) with purified proteins to validate the kinetics measured using the surface display. Positions, where CcdB mutations lead to slower rejuvenation rates, are largely involved in CcdA-binding, though there were several notable exceptions suggesting allostery. Mutations at these positions reduce the affinity towards CcdA, thereby slowing down the rejuvenation process. Mutations at GyrA14-interacting positions significantly enhanced rejuvenation rates, either due to reduced affinity or complete loss of CcdB binding to GyrA14. We examined the effect of different parameters (CcdA affinity, GyrA14 affinity, surface accessibilities, evolutionary conservation) on the rate of rejuvenation. Finally, we further validated the Ter-Seq results by monitoring the kinetics of ternary complex formation for individual CcdB mutants in solution by fluorescence resonance energy transfer (FRET) studies. 相似文献
943.
番木瓜是岭南四大名果之一,在我国东南部地区广泛种植,因其具有食用和药用双重价值,因此深受人们的青睐。果糖-6-磷酸,2-激酶/果糖-2,6-二磷酸酯酶(fructose-6-phosphate,2-kinase/fructose-2,6-bisphosphatase,F2KP)是一个独特的双功能酶,具有激酶功能域和酯酶功能域,能催化生物体内糖代谢的重要调节物果糖-2,6-二磷酸(Fru-2,6-P_(2))的合成和降解。为了研究番木瓜中编码该酶的基因CpF2KP的功能,得到目的蛋白尤为重要。本研究从番木瓜基因组中提取到CpF2KP基因的编码序列(coding sequence,CDS)序列,该基因CDS全长2274 bp。将该基因CDS全长扩增之后选用pGEX-4T-1载体进行原核表达。对载体pGEX-4T-1用EcoRⅠ和BamHⅠ进行双酶切,利用基因重组的方式将扩增序列构建到原核表达载体上。经过诱导条件探索,SDS-PAGE结果显示GST-CpF2KP重组蛋白的大小约为110 kDa,诱导CpF2KP蛋白表达的最适条件为:异丙基β-D-硫代半乳糖苷(isopropyl beta-D-thiogalactopyranoside,IPTG)浓度为0.5 mmol/L,温度28℃。对诱导后的CpF2KP蛋白进行纯化,得到了纯化的单一目的蛋白。此外,检测了该基因的组织表达特性发现该基因在种子中表达量最高,在果肉中表达量最低。该研究为进一步深入揭示番木瓜CpF2KP蛋白的功能及研究该基因参与的生物学过程提供了重要基础。 相似文献
944.
Qiulin Li Naoki Yamamoto Seiji Morisawa Akira Inoue 《Journal of cellular biochemistry》1993,51(4):458-464
Long-chain fatty acids and their acyl-CoA esters are potent inhibitors of nuclear thyroid hormone (T3) receptor in vitro. In the present study, we obtained evidence for acyl-CoA binding activity in the nuclear extract from rat liver. The activity sedimented at a position (3.5 S) identical with that of the T3 receptor, and the two activities sedimented together. Similarly, they coeluted on DEAE-Sephadex. After partial purification of the receptor, it was again inhibited strongly by acyl-CoAs. Heat stability and a partial trypsin digestion of the receptor both suggested that the action site of oleoyl-CoA overlapped the T3-binding domain of the receptor. In addition, thyroid hormone receptor β1, synthesized in vitro, bound oleoyl-CoA specifically and its T3-binding activity was inhibited. The dissociation constant for oleoyl-CoA binding to the partially purified receptor was 1.2 × 10?7 M. This value as well as its molecular size distinguished the nuclear binding sites from the cytoplasmic fatty acid/acyl-CoA binding proteins. Oleoyl-CoA had no effect on the glucocorticoid receptor, another member of the nuclear hormone-receptor superfamily. From these results, we propose that thyroid hormone receptor is a specific acyl-CoA binding protein of the cell nucleus. 相似文献
945.
A. B. Fulton 《Journal of cellular biochemistry》1993,52(2):148-152
The cytoskeleton of most cells is complex and spatially diverse. The mRNAs for some cytoskeletal proteins are localized, suggesting that synthesis of these proteins may occur at sites appropriate for function or assembly. mRNA concentrations were first observed for several oocyte and embryonic mRNAs. Some insight has been gained into the mechanisms that help to position these mRNAs. More surprising to some, many cytoskeletal mRNAs are also localized. Among them are mRNAs for actin, tubulin, intermediate filaments, and a variety of associated proteins. Different mRNAs in the same cell can be located in different places; the same mRNA can be located in different places; the same mRNA can be located differently at different times of development. For example, we observed vimentin mRNA in developing chicken muscle cultures by fluorescent in situ hybridization. We found that vimentin mRNA takes on a variety of positions during myogenesis, ending up located with its cognate protein at costameres. This last pattern is significant because it is too finely structured to have a function in the soluble phase and probably reflects contranslational assembly of this particular protein. Analogies can be made between oocyte or embryonic positions (animal/vegetal poles, oocyte cortex, and interior) and somatic cell positions (anterior/posterior and cell cortex/cell center). These analogies may point to conserved mechanisms for moving and retaining mRNA. Localization of cytoskeletal synthesis, through the mRNA or by other means, may prove as important for assembling and maintaining differentiated cytoskeletal structures and somatic cells as mRNA location is for organizing the embryo. Mechanisms that permit mRNA localization are likely to be conserved. 相似文献
946.
Jonathan Reizer Antonio H. Romano Josef Deutscher 《Journal of cellular biochemistry》1993,51(1):19-24
HPr of the Gram-positive bacterial phosphotransferase system (PTS) can be phosphorylated by an ATP-dependent protein kinase on a serine residue or by PEP-dependent Enzyme I on a histidyl residue. Both phosphorylation events appear to influence the metabolism of non-PTS carbon sources. Catabolite repression of the gluconate (gnt) operon of B. subtilis appears to be regulated by the former phosphorylation event, while glycerol kinase appears to be regulated by the latter phosphorylation reaction. The extent of our understanding of these processes will be described. © 1993 Wiley-Liss, Inc. 相似文献
947.
Christina Seisenberger Tobias Graf Sarah Sticht Markus Haindl Ulrich Mohn Harald Wegele Michael Wiedmann Stefanie Wohlrab 《Biotechnology and bioengineering》2023,120(1):184-193
Host cell proteins (HCPs) are inevitable process-related impurities in biotherapeutics commonly monitored by enzyme-linked immunosorbent assays (ELISAs). Of particular importance for their reliable detection are the anti-HCP polyclonal antibodies (pAbs), supposed to detect a broad range of HCPs. The present study focuses on the identification of suitable host animal species for the development of high-performance CHO-HCP ELISAs, assuming the generation of pAbs with adequate coverage and specificity. Hence, antibodies derived from immunization of sheep, goats, donkeys, rabbits, and chickens were compared concerning their amount of HCP-specific antibodies, coverage, and performance in a sandwich ELISA. Immunization of sheep, goats, donkeys, and rabbits met all test criteria, whereas the antibodies from chickens cannot be recommended based on the results of this study. Additionally, a mixture of antibodies from the five host species was prepared to assess if coverage and ELISA performance can be improved by a multispecies approach. Comparable results were obtained for the single- and multispecies ELISAs in different in-process samples, indicating no substantial improvement for the latter in ELISA performance while raising ethical and financial concerns. 相似文献
948.
Theodoros K. Karamanos 《Biopolymers》2023,114(3):e23530
Coevolution between protein residues is normally interpreted as direct contact. However, the evolutionary record of a protein sequence contains rich information that may include long-range functional couplings, couplings that report on homo-oligomeric states or even conformational changes. Due to the complexity of the sequence space and the lack of structural information on various members of a protein family, it has been difficult to effectively mine the additional information encoded in a multiple sequence alignment (MSA). Here, taking advantage of the recent release of the AlphaFold (AF) database we attempt to identify coevolutionary couplings that cannot be explained simply by spatial proximity. We propose a simple computational method that performs direct coupling analysis on a MSA and searches for couplings that are not satisfied in any of the AF models of members of the identified protein family. Application of this method on 2012 protein families suggests that ~12% of the total identified coevolving residue pairs are spatially distant and more likely to be disordered than their contacting counterparts. We expect that this analysis will help improve the quality of coevolutionary distance restraints used for structure determination and will be useful in identifying potentially functional/allosteric cross-talk between distant residues. 相似文献
949.
Pamela F. Olson Tuula Salo Katherine Garrison John H. Fessler 《Journal of cellular biochemistry》1993,51(3):353-359
A cDNA encoding the Drosophila melanogaster acidic ribosomal protein rpA2 was cloned and sequenced. rpA2 is homologous to the Artemia salina acidic ribosomal protein eL12′. In situ hybridization to salivary gland polytene chromosomes localizes the rpA2 gene to band 21C. It is a single copy gene, with an mRNA of 0.8 kb. Two-dimensional gel electrophoresis of Drosophila ribosomal proteins followed by immuno-blotting showed that the rpA2 protein has an apparent relative mobility in SDS of 17 kD and an isoelectric point less than pH 5.0. Although the Drosophila gene rp21C may be the same as rpA2, the reported sequences differ. Comparisons of the aligned nucleotide sequences coding for the acidic ribosomal proteins rpA1 and rpA2 of Drosophila with those of other eukaryotes support the view of two separate, though closely related, groups of acidic proteins. Comparison with the Artemia homologues suggests that nucleotide identity may have been conserved by some constraint that acts in addition to the requirement for substantial similarity of amino acid sequences. © 1993 Wiley-Liss, Inc. 相似文献
950.
Gerald Platteau Guido Stroehlein James Van Alstine Masayoshi Nagaya 《Biotechnology and bioengineering》2023,120(10):2907-2916
Prepacked chromatography columns and cassette filtration units offer many advantages in bioprocessing. These include reduced labor costs and processing times, ease of storage, and enhanced process flexibility. Rectangular formats are particularly attractive as they can be easily stacked and multiplexed together for continuous processing. Cylindrical chromatography beds have dominated bioprocessing even though their bed support and pressure-flow performance vary with bed dimensions. This work presents the performance of novel, rhombohedral chromatography devices with internally supported beds. They are compatible with existing chromatography workstations and can be packed with any standard commercial resin. The devices offer pressure-flow characteristics independent of container-volume, simple multiplexing, and separation performance comparable to cylindrical columns. Their bi-planar, internal bed support allows mechanically less-rigid resins to be used at up to four times higher maximal linear velocities, and productivities approaching 200 g/L/h for affinity resins, compared to the 20 g/L/h typical of many column-based devices. Three 5 L devices should allow processing of up to 3 kg of monoclonal antibody per hour. 相似文献