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131.
Clémentine Aguirre Tim ten Brink Olivier Cala Jean-François Guichou Isabelle Krimm 《Journal of biomolecular NMR》2014,60(2-3):147-156
The fragment-based drug design approach consists of screening libraries of fragment-like ligands, to identify hits that typically bind the protein target with weak affinity ( \(100\,\upmu \hbox {M}\) –5 mM). The determination of the protein–fragment complex 3D structure constitutes a crucial step for uncovering the key interactions responsible for the protein–ligand recognition, and for growing the initial fragment into potent active compounds. The vast majority of fragments are aromatic compounds that induce chemical shift perturbations (CSP) on protein NMR spectra. These experimental CSPs can be quantitatively used to guide the ligand docking, through the comparison between experimental CSPs and CSP back-calculation based on the ring current effect. Here we implemented the CSP back-calculation into the scoring function of the program PLANTS. We compare the results obtained with CSPs measured either on amide or aliphatic protons of the human peroxiredoxin 5. We show that the different kinds of protons lead to different results for resolving the 3D structures of protein–fragment complexes, with the best results obtained with the \(\hbox {H}_{\alpha }\) protons. 相似文献
132.
Jennifer H Humphreys Jessica AB van Nies Jackie Chipping Tarnya Marshall Annette HM van der Helm-van Mil Deborah PM Symmons Suzanne MM Verstappen 《Arthritis research & therapy》2014,16(6)
Introduction
This study aimed to investigate rheumatoid factor (RF) and anti-citrullinated protein antibody (ACPA) status and levels as predictors of mortality in two large cohorts of patients with early inflammatory arthritis (EIA).Methods
Data from the Norfolk Arthritis Register (NOAR) and Leiden Early Arthritis Clinic (EAC) cohorts were used. At baseline, patients had demographic data and smoking status recorded; RF, ACPA and inflammatory markers were measured in the local laboratories. Patients were flagged with national death registers until death or censor date. Antibody status was stratified as negative, low or high positive by RF and ACPA levels individually. In addition, patients were grouped as seronegative, RF positive, ACPA positive or double antibody (RF and ACPA) positive. Cox regression models explored associations between antibody status and mortality adjusting for age, sex, smoking status, inflammatory markers and year of enrolment.Results
A total of 4962 patients were included, 64% were female. Median age at onset was 56 (NOAR) and 54 (EAC) years. In NOAR and EAC respectively, 35% and 42% of patients were ACPA/RF positive. When antibody status was stratified as negative, low or high positive, there were no consistent findings between the two cohorts. Double antibody positivity was associated with excess mortality in both cohorts compared to seronegative patients: NOAR and EAC respective adjusted HR (95% confidence interval) 1.35 (1.09 to 1.68) and 1.58 (1.16 to 2.15).Conclusions
Patients with EIA who are seropositive for both RF and ACPA have increased mortality compared to those who are single positive or seronegative. Antibody level in seropositive patients was not consistently associated with excess mortality.Electronic supplementary material
The online version of this article (doi:10.1186/s13075-014-0483-3) contains supplementary material, which is available to authorized users. 相似文献133.
Clémentine Aguirre Tim ten Brink Jean-Fran?ois Guichou Olivier Cala Isabelle Krimm 《PloS one》2014,9(7)
Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD) experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP) calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model. 相似文献
134.
Chevonne D Eversley Tavia Clark Yuying Xie Jill Steigerwalt Timothy A Bell Fernando PM de Villena David W Threadgill 《BMC genetics》2010,11(1):1-6
Background
Sheep carcasses with yellow fat are sporadically observed at Norwegian slaughter houses. This phenomenon is known to be inherited as a recessive trait, and is caused by accumulation of carotenoids in adipose tissue. Two enzymes are known to be important in carotenoid degradation in mammals, and are therefore potential candidate genes for this trait. These are beta-carotene 15,15'-monooxygenase 1 (BCMO1) and the beta-carotene oxygenase 2 (BCO2).Results
In the present study the coding region of the BCMO1 and the BCO2 gene were sequenced in yellow fat individuals and compared to the corresponding sequences from control animals with white fat. In the yellow fat individuals a nonsense mutation was found in BCO2 nucleotide position 196 (c.196C>T), introducing a stop codon in amino acid position 66. The full length protein consists of 575 amino acids. In spite of a very low frequency of this mutation in the Norwegian AI-ram population, 16 out of 18 yellow fat lambs were found to be homozygous for this mutation.Conclusion
In the present study a nonsense mutation (c.196C>T) in the beta-carotene oxygenase 2 (BCO2) gene is found to strongly associate with the yellow fat phenotype in sheep. The existence of individuals lacking this mutation, but still demonstrating yellow fat, suggests that additional mutations may cause a similar phenotype in this population. The results demonstrate a quantitatively important role for BCO2 in carotenoid degradation, which might indicate a broad enzyme specificity for carotenoids. Animals homozygous for the mutation are not reported to suffer from any negative health or development traits, pointing towards a minor role of BCO2 in vitamin A formation. Genotyping AI rams for c.196C>T can now be actively used in selection against the yellow fat trait. 相似文献135.
136.
A coiled capillary viscometer for blood. 总被引:1,自引:0,他引:1
137.
Molecular evolution of bacteriophages: evidence of selection against the recognition sites of host restriction enzymes 总被引:12,自引:0,他引:12
Restriction enzymes produced by bacteria serve as a defense against
invading bacteriophages, and so phages without other protection would be
expected to undergo selection to eliminate recognition sites for these
enzymes from their genomes. The observed frequencies of all restriction
sites in the genomes of all completely sequenced DNA phages (T7, lambda,
phi X174, G4, M13, f1, fd, and IKe) have been compared to expected
frequencies derived from trinucleotide frequencies. Attention was focused
on 6-base palindromes since they comprise the typical recognition sites for
type II restriction enzymes. All of these coliphages, with the exception of
lambda and G4, exhibit significant avoidance of the particular sequences
that are enterobacterial restriction sites. As expected, the sequenced
fraction of the genome of phi 29, a Bacillus subtilis phage, lacks Bacillus
restriction sites. By contrast, the RNA phage MS2, several viruses that
infect eukaryotes (EBV, adenovirus, papilloma, and SV40), and three
mitochondrial genomes (human, mouse, and cow) were found not to lack
restriction sites. Because the particular palindromes avoided correspond
closely with the recognition sites for host enzymes and because other
viruses and small genomes do not show this avoidance, it is concluded that
the effect indeed results from natural selection.
相似文献
138.
The reciprocal position of sexual organs in complementary floral morphs is central to our understanding of heterostyly. Reciprocity indices are used to quantify the spatial match between complementary sex organs, but previous indices fail to appropriately account for intra-population variation in sex organ positions. In this study, we examine how an increase in intra-population variation in sex organ heights affects reciprocity and consequently reproductive success. We formulated a reciprocity index that incorporates this variation and asked if estimates of reciprocity can predict reproductive success in naturally occurring heterostylous populations. We developed a reciprocity index that assumed pollen transfer success equalled one for a perfectly matched stigma–anther pair, and decreased to zero with increasing mismatch. We examined the relationship between intra-population variation in organ position and reciprocity, compared previously proposed indices using simulated populations and empirical data from natural populations, and tested the ability of the indices to predict reproductive success. We observed that when differences between mean complementary sex-organ heights are small, increasing intra-population variation in heights resulted in a decrease in reciprocity. However, when this difference is larger, reciprocity increased, reached a peak, and then decreased with increasing variation. Previous indices failed to capture this behavior. Seed set was positively related to reciprocity for our index. These results challenge the current understanding that increasing variation in sex-organ heights will always decrease reciprocity in heterostylous populations. This may help explain why heterostylous systems exhibit and tolerate high amounts of intra-population variation in sex organ heights. 相似文献
139.
140.