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111.
The computational identification of all the low energy structures of a peptide given only its sequence is not an easy task even for small peptides,due to the multiple-minima problem and combinatorial explosion. We have developed an algorithm, called the MOLS technique,that addresses this problem, and have applied it to a number of different aspects of the study of peptide and protein structure. Conformational studies of oligopeptides, including loop sequences in proteins have been carried out using this technique. In general the calculations identified all the folds determined by previous studies,and in addition picked up other energetically favorable structures. The method was also used to map the energy surface of the peptides. In another application, we have combined the MOLS technique, using it to generate a library of low energy structures of an oligopeptide, with a genetic algorithm to predict protein structures. The method has also been applied to explore the conformational space of loops in protein structures.Further, it has been applied to the problem of docking a ligand in its receptor site, with encouraging results. 相似文献
112.
Pal C Dey S Mahato SK Vinayagam J Pradhan PK Giri VS Jaisankar P Hossain T Baruri S Ray D Biswas SM 《Bioorganic & medicinal chemistry letters》2007,17(17):4924-4928
3,3'-Diindolylmethane (DIM) derivatives 3a-k, prepared in one-pot from indoles 1a-k and hexamethylenetetramine (2) using ionic liquid [Bmim]BF(4) as eco-friendly recyclable solvent as well as catalyst, showed good plant growth promoting activity on Oryza sativa. Among the DIM derivatives synthesized 3c shows potent auxin like growth promoting activity. 相似文献
113.
Influence of gap size and soil properties on microbial biomass in a subtropical humid forest of north-east India 总被引:9,自引:0,他引:9
We examined the effects of treefall gap size and soil properties on microbial biomass dynamics in an undisturbed mature-phase
humid subtropical broadleaved forest in north-east India. Canopy gaps had low soil moisture and low microbial biomass suggesting
that belowground dynamics accompanied changes in light resources after canopy opening. High rainfall in the region causes
excessive erosion/leaching of top soil and eventually soil fertility declines in treefall gaps compared to understorey. Soil
microbial population was less during periods when temperature and moisture conditions are low, while it peaked during rainy
season when the litter decomposition rate is at its peak on the forest floor. Greater demand for nutrients by plants during
rainy season (the peak vegetative growth period) limited the availability of nutrients to soil microbes and, therefore, low
microbial C, N and P. Weak correlations were also obtained for the relationships between microbial C, N and P and soil physico–chemical
properties. Gap size did influence the microbial nutrients and their contribution to soil organic carbon, total Kjeldhal nitrogen
and available-P. Contribution of microbial C to soil organic carbon, microbial N to total nitrogen were similar in both treefall
gaps and understorey plots, while the contribution of microbial P to soil available-P was lower in gap compared to the understorey.
These results indicate that any fluctuation in microbial biomass related nutrient cycling processes in conjunction with the
associated microclimate variation may affect the pattern of regeneration of tree seedlings in the gaps and hence be related
with their size.
This revised version was published online in June 2006 with corrections to the Cover Date. 相似文献
114.
von Wronski MA Raju N Pillai R Bogdan NJ Marinelli ER Nanjappan P Ramalingam K Arunachalam T Eaton S Linder KE Yan F Pochon S Tweedle MF Nunn AD 《The Journal of biological chemistry》2006,281(9):5702-5710
Tuftsin, Thr-Lys-Pro-Arg (TKPR), is an immunostimulatory peptide with reported nervous system effects as well. We unexpectedly found that tuftsin and a higher affinity antagonist, TKPPR, bind selectively to neuropilin-1 and block vascular endothelial growth factor (VEGF) binding to that receptor. Dimeric and tetrameric forms of TKPPR had greatly increased affinity for neuropilin-1 based on competition binding experiments. On endothelial cells tetrameric TKPPR inhibited the VEGF(165)-induced autophosphorylation of vascular endothelial growth factor receptor-2 (VEGFR-2) even though it did not directly inhibit VEGF binding to VEGFR-2. Homology between exon 8 of VEGF and TKPPR suggests that the sequence coded for by exon 8 may stabilize VEGF binding to neuropilin-1 to facilitate signaling through VEGFR-2. Given the overlap between processes involving neuropilin-1 and tuftsin, we propose that at least some of the previously reported effects of tuftsin are mediated through neuropilin-1. 相似文献
115.
Aikkal Riju M. K. Rajesh P. T. P. Fasila Sherin A. Chandrasekar S. Elain Apshara Vadivel Arunachalam 《Journal of genetics》2009,88(2):217-225
Expressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene
expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial
crop of humid tropics. Cacao EST sequences, as available in the public domain, were downloaded and made into contigs. Microsatellites
were located in these ESTs and contigs using five softwares (MISA, TRA, TROLL, SSRIT and SSR primer). MISA gave maximum coverage
of SSRs in cacao ESTs and contigs, although TRA was able to detect higher order (>5-mer) repeats. The frequency of SSRs was
one per 26.9 kb in the known set of ESTs. One-third of the repeats in EST-contigs were found to be trimeric. A few rare repeats
like 21-mer repeat were also located. A/T repeats were most abundant among the mononucleotide repeats and the AG/GA/TC/CT
type was the most frequent among dimerics. Flanking primers were designed using Primer3 program and verified experimentally
for PCR amplification. The results of the study are made available freely online database (). Seven primer pairs amplified genomic DNA isolated from leaves were used to screen a representative set of 12 accessions
of cacao. 相似文献
116.
Sulaiman Ali Alharbi Saleh Hussein Salmen Arunachalam Chinnathambi Naiyf S. Alharbi M.E. Zayed Bassam O. Al-Johny Milton Wainwright 《Saudi Journal of Biological Sciences》2016,23(2):268-271
The present study was carried out, using standard techniques, to identify and count the bacterial contamination of hand air dryers, used in washrooms. Bacteria were isolated from the air flow, outlet nozzle of warm air dryers in fifteen air dryers used in these washrooms. Bacteria were found to be relatively numerous in the air flows. Bacterially contaminated air was found to be emitted whenever a warm air dryer was running, even when not being used for hand drying. Our investigation shows that Staphylococcus haemolyticus, Micrococcus luteus, Pseudomonas alcaligenes, Bacillus cereus and Brevundimonad diminuta/vesicularis were emitted from all of the dryers sampled, with 95% showing evidence of the presence of the potential pathogen S. haemolyticus. It is concluded that hot air dryers can deposit pathogenic bacteria onto the hands and body of users. Bacteria are distributed into the general environment whenever dryers are running and could be inhaled by users and none-users alike. The results provide an evidence base for the development and enhancement of hygienic hand drying practices. 相似文献
117.
U Arunachalam V Massey C S Vaidyanathan 《The Journal of biological chemistry》1992,267(36):25848-25855
p-Hydroxyphenylacetate-3-hydroxylase, an inducible enzyme isolated from the soil bacterium Pseudomonas putida, catalyzes the conversion of p-hydroxyphenylacetate to 3,4-dihydroxyphenylacetate. The enzyme requires two protein components: a flavoprotein and a colorless protein referred to as the coupling protein. The flavoprotein alone in the presence of p-hydroxyphenylacetate and substrate analogs catalyzes the wasteful oxidation of NADH with the stoichiometric generation of H2O2. A 1:1 complex of the flavoprotein and coupling protein is required for stoichiometric product formation. Such complex formation also eliminates the nonproductive NADH oxidase activity of the flavoprotein. A new assay measuring the product formation activity of the enzyme was developed using homoprotocatechuate-2,3-dioxygenase, as monitoring the oxidation of NADH was not sufficient to demonstrate enzyme activity. The coupling protein does not seem to have any redox center in it. Thus, this 2-component flavin hydroxylase resembles the other aromatic hydroxylases in that the only redox chromophore present is FAD. 相似文献
118.
119.
Cultivation based and culture independent molecular approaches were used to characterize the composition and structure of
bacterial community from a natural warm spring in the Western Ghats, a biodiversity ‘hotspot’. Dilution plating was done on
three types of media with varying nutrient levels. Relatively nutritionally poor medium supported growth of highest number
of bacteria (4.98 × 103 ml−1) compared to nutritionally rich media. On the basis of different morphological features on the plate, 62 aerobic and heterotrophic
bacterial strains were isolated and their 16S rRNA genes were sequenced and analyzed. On the basis of sequence similarity
these isolates were found to be distributed in 21 different genera belonging to Proteobacteria (58%) followed by Firmicutes (26%), Actinobacteria (13%) and Bacteroidetes (3%). Amplification of 16S rRNA gene of the community DNA using eubacterial primers, followed by cloning and sequencing revealed
that predominant members of the habitat belong to the phylum Cyanobacteria (60%) followed by Proteobacteria (19.5%), Bacteroidetes (6.67%), Actinobacteria (4.4%) and Firmicutes (2.2%) and small ribosomal subunit of a plastid (of Chlorophyta, 2.2%). 相似文献
120.
Palanichamy Esakkiraj Suppiah Sankaralingam Raj Usha Arunachalam Palavesam Grasian Immanuel 《Annals of microbiology》2011,61(4):749-755
The possibility of utilising anchovy waste meal as a substrate for protease production by the fish gut isolate Serratia proteamaculans AP-CMST was assessed through solid-state fermentation. A time course for protease production revealed 72 h to be the optimum duration for higher production (146.24 U/g). The most suitable pH, temperature and moisture level observed for higher protease production were pH 7 (123.5 U/g), 30°C (97.22 U/g) and 75% (126.7 U/g), respectively. Protease production by S. proteamaculans AP-CMST was high in medium with added xylose (198.21 U/g), peptone (118.42 U/g), Triton X-100 (152.56 U/g) and manganese sulphate (178.33 U/g) when compared to other tested medium components. The halotolerancy of S. proteamaculans AP-CMST for protease production was 4% sodium chloride (155.65 U/g). Enzyme recovery from fermented anchovy waste meal was greatest (130.52 U/g) when 10% ethyl acetate was used as the extractant, and the optimum time range for extraction was 90–120 min. 相似文献