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排序方式: 共有725条查询结果,搜索用时 15 毫秒
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Huixin Wang Dr. Michael G. Leeming Dr. Junming Ho Dr. William A. Donald 《Chemistry (Weinheim an der Bergstrasse, Germany)》2019,25(3):823-834
Predicting the fragmentation patterns of proteins would be beneficial for the reliable identification of intact proteins by mass spectrometry. However, the ability to accurately make such predictions remains elusive. An approach to predict the specific cleavage sites in whole proteins resulting from collision-induced dissociation by use of an improved electrostatic model for calculating the proton configurations of highly-charged protein ions is reported. Using ubiquitin, cytochrome c, lysozyme and β-lactoglobulin as prototypical proteins, this approach can be used to predict the fragmentation patterns of intact proteins. For sufficiently highly charged proteins, specific cleavages occur near the first low-basicity amino acid residues that are protonated with increasing charge state. Hybrid QM/QM′ (QM=quantum mechanics) and molecular dynamics (MD) simulations and energy-resolved collision-induced dissociation measurements indicated that the barrier to the specific dissociation of the protonated amide backbone bond is significantly lower than competitive charge remote fragmentation. Unlike highly charged peptides, the protons at low-basicity sites in highly charged protein ions can be confined to a limited sequence of low-basicity amino acid residues by electrostatic repulsion, which results in highly specific fragmentation near the site of protonation. This research suggests that the optimal charge states to form specific sequence ions of intact proteins in higher abundances than the use of less specific ion dissociation methods can be predicted a priori. 相似文献
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从细胞穿膜肽(CPP)的分类、内化机制、与货物的连接和应用四个方面讲述目前人们在对细胞穿膜肽的研究上已经取得的成果。细胞穿膜肽是一种能穿过细胞膜的短肽,可分为阳离子型肽、两亲性肽和疏水性肽。细胞穿膜肽的内化机制主要有内吞作用、直接渗透、依赖于糖蛋白的内化机制和依赖于浓度的内化机制等。近年来,人们合成了多种有实际应用价值的CPP-货物复合物,在细胞穿膜肽的应用上,取得了很多进展和突破。科学家们主要研究将细胞穿膜肽应用于药物递送和细胞成像。 相似文献
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In Situ Proteome Profiling and Bioimaging Applications of Small‐Molecule Affinity‐Based Probes Derived From DOT1L Inhibitors 下载免费PDF全文
Biwei Zhu Dr. Hailong Zhang Sijun Pan Chenyu Wang Dr. Jingyan Ge Prof. Dr. Jun‐Seok Lee Prof. Dr. Shao Q. Yao 《Chemistry (Weinheim an der Bergstrasse, Germany)》2016,22(23):7824-7836
DOT1L is the sole protein methyltransferase that methylates histone H3 on lysine 79 (H3K79), and is a promising drug target against cancers. Small‐molecule inhibitors of DOT1L such as FED1 are potential anti‐cancer agents and useful tools to investigate the biological roles of DOT1L in human diseases. FED1 showed excellent in vitro inhibitory activity against DOT1L, but its cellular effect was relatively poor. In this study, we designed and synthesized photo‐reactive and “clickable” affinity‐based probes (AfBPs), P1 and P2 , which were cell‐permeable and structural mimics of FED1 . The binding and inhibitory effects of these two probes against DOT1L protein were extensively investigated in vitro and in live mammalian cells (in situ). The cellular uptake and sub‐cellular localization properties of the probes were subsequently studied in live‐cell imaging experiments, and our results revealed that, whereas both P1 and P2 readily entered mammalian cells, most of them were not able to reach the cell nucleus where functional DOT1L resides. This offers a plausible explanation for the poor cellular activity of FED1 . Finally with P1 / P2 , large‐scale cell‐based proteome profiling, followed by quantitative LC‐MS/MS, was carried out to identify potential cellular off‐targets of FED1 . Amongst the more than 100 candidate off‐targets identified, NOP2 (a putative ribosomal RNA methyltransferase) was further confirmed to be likely a genuine off‐target of FED1 by preliminary validation experiments including pull‐down/Western blotting (PD/WB) and cellular thermal shift assay (CETSA). 相似文献
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Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high‐throughput structural studies on proteins 下载免费PDF全文
Ramakrishna V. Hosur 《Magnetic resonance in chemistry : MRC》2015,53(2):79-87
Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence‐specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D‐hNCO canH and (3,2)D‐hN coCA nH – which enhance the previously described 2D NMR‐based assignment methods quite significantly. Both the experiments can be recorded in just about 2–3 h each and hence would be of immense value for high‐throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha‐helical bovine apo calbindin‐D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web‐based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high‐throughput structural studies of proteins. Copyright © 2014 John Wiley & Sons, Ltd. 相似文献
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Romain Tessier Raj Kumar Nandi Brendan G. Dwyer Daniel Abegg Charlotte Sornay Javier Ceballos Stphane Erb Sarah Cianfrani Alain Wagner Guilhem Chaubet Alexander Adibekian Jerome Waser 《Angewandte Chemie (International ed. in English)》2020,59(27):10961-10970
Current approaches to introduce terminal alkynes for bioorthogonal reactions into biomolecules still present limitations in terms of either reactivity, selectivity, or adduct stability. We present a method for the ethynylation of cysteine residues based on the use of ethynylbenziodoxolone (EBX) reagents. The acetylene group is directly introduced onto the thiol group of cysteine and can be used for copper‐catalyzed alkyne‐azide cycloaddition (CuAAC) without further processing. Labeling proceeded with reaction rates comparable to or higher than the most often used iodoacetamide on peptides or maleimide on the antibody trastuzumab, and high cysteine selectivity was observed. The reagents were also used in living cells for cysteine proteomic profiling and displayed improved coverage of the cysteinome compared to previously reported iodoacetamide or hypervalent iodine reagents. Fine‐tuning of the EBX reagents allows optimization of their reactivity and physical properties. 相似文献
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