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121.
All of the α-subgroups share similarity in their sequence and structure but different in the toxicity to various voltage-gated sodium channels (VGSCs). We modeled the first 3D structural model of the Od1 based on BmK M1 using homology modeling. The reliability of model for more investigation and compare to BmK M1 has been examined and confirmed. Then the model structure is further refined by energy minimization and molecular dynamics methods. The purpose of this modeling and simulation is comparison toxicity of two mentioned toxins by investigation structural feature of functional regions including core domain, 5-turn and C-terminal which make NC domain. In the one hand, it is intriguing that Od1 in comparison to BmK M1 shows same solvent accessible surface area (SASA) in 5-turn region but a little more exposed and feasibility (more SASA) in C-terminal region and key functional residues of C-terminal such as positive residues Arg58, lys62 and Arg (His)64. These data suggested that Od1 has similarity with BmK M1 but has more toxicity to sodium channel. In the other hand 5-turn proximity of C-terminal to 5-turn in BmK M1with cis peptide bond is less than Od1 without cis peptide bond which is a confirmation with experimental data about BmK M1.A better understanding of the 3-D structure of Od1and comparison to BmK M1 will be helpful for more investigation of functional characters action of natural toxins with a specialized role for VGSCs. 相似文献
122.
Firooznia F Cheung AW Brinkman J Grimsby J Gubler ML Hamid R Marcopulos N Ramsey G Tan J Wen Y Sarabu R 《Bioorganic & medicinal chemistry letters》2011,21(7):1933-1936
The highly potent but modestly selective N-(2-amino-4-methoxy-benzothiazol-7-yl)-N-ethyl-acetamide derivative 2 was selected as the starting point for the design of novel selective A2B antagonists, due to its excellent potency, and good drug-like properties. A series of compounds containing nonaromatic amides or ureas of five- or six-membered rings, and also bearing an m-trifluoromethyl-phenyl group (shown to impart superior potency) was prepared and evaluated for their selectivity against the A2A and A1 receptors. This work resulted in the identification of compound 30, with excellent potency and high selectivity against both A2A and A1 receptors. 相似文献
123.
Leimgruber A Ferber M Irving M Hussain-Kahn H Wieckowski S Derré L Rufer N Zoete V Michielin O 《PloS one》2011,6(10):e26301
TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling. 相似文献
124.
Qadri Q Sameer AS Shah ZA Hamid A Alam S Manzoor S Siddiqi MA 《Genetics and molecular research : GMR》2011,10(4):3038-3045
Glutathione-S-transferase P1 (GSTP1) is a critical enzyme of the phase II detoxification pathway. One of the common functional polymorphisms of GSTP1 is A→G at nucleotide 313, which results in an amino acid substitution (Ile105Val) at the substrate binding site of GSTP1 and reduces catalytic activity of GSTP1. To investigate the GSTP1 Ile105Val genotype frequency in prostate cancer cases in the Kashmiri population, we designed a case-control study, in which 50 prostate cancer cases and 45 benign prostate hyperplasia cases were studied for GSTP1 Ile105Val polymorphism, compared to 80 controls taken from the general population, employing the PCR-RFLP technique. We found the frequency of the three different genotypes of GSTP1 Ile105Val in our ethnic Kashmir population, i.e., Ile/Ile, Ile/Val and Val/Val, to be 52.4, 33.3 and 14.3% among prostate cancer cases, 48.5, 37.5 and 14% among benign prostate hyperplasia cases and 73.8, 21.3 and 5% in the control population, respectively. There was a significant association between the GSTP1 Ile/Val genotype and the advanced age group among the cases. We conclude that GSTP1 Ile/Val polymorphism is involved in the risk of prostate cancer development in our population. 相似文献
125.
Nagwa Rashed Hamida Abdel Hamid El Sayed Ramadan El Sayed H. El Ashry 《Nucleosides, nucleotides & nucleic acids》2013,32(8):1373-1384
ABSTRACT Cyclodehydrogenation of the ethylidene derivative of (5-methyl-1,2,4-triazino[5,6-b]indol-3-yl)hydrazine (1) gave the angular isomer, 1,10-dimethyl-1,2,4-triazolo[3′,4′:3,4][1,2,4]triazino[5,6-b]indole (4). The linear isomer, 3,10-dimethyl-1,2,4-triazolo[4′,3′:2,3][1,2,4]triazino[5,6-b]indole (7) could be prepared regioselectively by the cyclodehydration of the acetyl derivative of 1. The cyclodehydrogenation was extended to the monosaccharide derivatives of 1. The role of the N-methyl group on the site of annellation has been discussed. 相似文献
126.
Shakibaie M Forootanfar H Mollazadeh-Moghaddam K Bagherzadeh Z Nafissi-Varcheh N Shahverdi AR Faramarzi MA 《Biotechnology and applied biochemistry》2010,57(2):71-75
The application of green-synthesis principles is one of the most impressive research fields for the production of nanoparticles. Different kinds of biological systems have been used for this purpose. In the present study, AuNPs (gold nanoparticles) were prepared within a short time period using a fresh cell extract of the marine microalga Tetraselmis suecica as a reducing agent of HAuCl4 (chloroauric acid) solution. The UV-visible spectrum of the aqueous medium containing AuNPs indicated a peak at 530 nm, corresponding to the surface plasmon absorbance of AuNPs. The X-ray diffraction pattern also showed a Bragg reflection related to AuNPs. Fourier-transform infrared spectroscopy was performed for analysis of surface functional groups of AuNPs. Transmission electron microscopy and particle-size-distribution patterns determined by the laser-light-scattering method confirmed the formation of well-dispersed AuNPs. The most frequent size of particles was 79 nm. 相似文献
127.
Abdel Hamid A. Khedr Mamdouh S. Serag Mamdouh M. Nemat-Alla Amina Z. Abo El-Naga Reham M. Nada W. Paul Quick Gaber M. Abogadallah 《Acta Physiologiae Plantarum》2011,33(5):1769-1784
In the present study, Na+ manipulating genes could contribute not only to ion homeostasis but also to growth stimulation with exposing the halophyte
Atriplex halimus L. to moderate NaCl concentration. The stimulation of growth was attributed to Na+ accumulation inside the vacuole leading to increase leaf cell size as well as accelerate leaf cell division. Increasing the
assimilatory surface could result in enhancing the photosynthetic rate. The reduction of A. halimus growth compared to optimum growth at 50 and 200 mM NaCl could be attributed to osmotic effect rather than the ionic one of
salt stress. The inhibition of photosynthesis seemed to be resulted from limitation of CO2 due to the osmotic effect on stomatal conductance rather than the activity loss of photosynthetic machinery. The depletion
of starch content along with the increase in sucrose content could imply that photosynthesis may be a limiting for A. halimus growth. The fast coordinate induction of Na+ manipulating genes could reveal that the tolerance of A. halimus to high concentrations evolved from its ability to regulate and control Na+ influx and efflux. V-H
+-PPase may play a vital role in A. halimus tolerance to osmotic and/or ionic stress due to its kinetics of induction. It seemed that H+-ATPase plays a pivotal role in A. halimus tolerance to stress due to the increase in its protein level was detected with all NaCl concentrations as well as with PEG
treatments. Both of these genes might be useful in improving stress tolerance in transgenic crops. 相似文献
128.
129.