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21.
Strong solvent signals lead to a disappearance of weak protein signals close to the solvent resonance frequency and to base plane variations all over the spectrum. AUREMOL-SSA provides an automated approach for solvent artifact removal from multidimensional NMR protein spectra. Its core algorithm is based on singular spectrum analysis (SSA) in the time domain and is combined with an automated base plane correction in the frequency domain. The performance of the method has been tested on synthetic and experimental spectra including two-dimensional NOESY and TOCSY spectra and a three-dimensional 1H,13C-HCCH-TOCSY spectrum. It can also be applied to frequency domain spectra since an optional inverse Fourier transformation is included in the algorithm.  相似文献   
22.
The leech protein Saratin from Hirudo medicinalis prevents thrombocyte aggregation by interfering with the first binding step of the thrombocytes to collagen by binding to collagen. We solved the three-dimensional structure of the leech protein Saratin in solution and identified its collagen binding site by NMR titration experiments. The NMR structure of Saratin consists of one α-helix and a five-stranded β-sheet arranged in the topology ββαβββ. The C-terminal region, of about 20 amino acids in length, adopts no regular structure. NMR titration experiments with collagen peptides show that the collagen interaction of Saratin takes place in a kind of notch that is formed by the end of the α-helix and the β-sheet. NMR data-driven docking experiments to collagen model peptides were used to elucidate the putative binding mode of Saratin and collagen. Mainly, parts of the first and the end of the fifth β-strand, the loop connecting the α-helix and the third β-strand, and a short part of the loop connecting the fourth and fifth β-strand participate in binding.  相似文献   
23.
24.
Primates have long been used as indicator species for assessing overall ecosystem health. However, area‐wide census methods are time consuming, costly, and not always feasible under many field conditions. Therefore, it is important to establish whether monitoring a subset of a population accurately reflects demographic changes occurring in the population at large. Over the past 35 years, we have conducted 15 area‐wide censuses in Sector Santa Rosa, Costa Rica. These efforts have revealed important trends in population growth patterns of capuchin monkeys following the protection and subsequent regeneration of native forests. During this same period, we have also intensively studied a subset of the capuchin groups. Comparing these two datasets, we investigate whether the population structures of the closely monitored groups are reliable indicators of area‐wide demographic patterns. We compare the overall group size and the individual age/sex class compositions of study groups and nonstudy groups (i.e., those contacted during area‐wide censuses only). Our study groups contained more individuals overall with a larger proportion of infants, and there were indications that the proportion of adult and subadult males was lower. These differences can be ascribed either to sampling errors or real differences attributable to human presence and/or better habitat quality for the study groups. No other sex/age classes differed, and major demographic changes were simultaneously evident in both study and nonstudy groups. This study suggests that the Santa Rosa capuchin population is similarly impacted by large‐scale ecological patterns observable within our study groups.  相似文献   
25.
For the Ras-binding domain of the protein kinase Byr2, only a limited number of NOE contacts could be initially assigned unambiguously, as the quality of the NOESY spectra was too poor. However, the use of residual (1)H-(15)N dipolar couplings in the beginning of the structure determination process allows to overcome this problem. We used a three-step recipe for this procedure. A previously unknown structure could be calculated reasonably well with only a limited number of unambiguously assigned NOE contacts.  相似文献   
26.
Summary A generally applicable method for the automated classification of 2D NMR peaks has been developed, based on a Bayesian approach coupled to a multivariate linear discriminant analysis of the data. The method can separate true NMR signals from noise signals, solvent stripes and artefact signals. The analysis relies on the assumption that the different signal classes have different distributions of specific properties such as line shapes, line widths and intensities. As to be expected, the correlation network of the distributions of the selected properties affects the choice of the discriminant function and the final selection of signal properties. The classification rule for the signal classes was deduced from Bayes's theorem. The method was successfully tested on a NOESY spectrum of HPr protein from Staphylococcus aureus. The calculated probabilities for the different signal class memberships are realistic and reliable, with a high efficiency of discrimination between peaks that are true NOE signals and those that are not.  相似文献   
27.
Summary AURELIA is an advanced program for the computer-aided evaluation of two-, three- and four-dimensional NMR spectra of any type of molecule. It can be used for the analysis of spectra of small molecules as well as for evaluation of complicated spectra of biological macromolecules such as proteins. AURELIA is highly interactive and offers a large number of tools, such as artefact reduction, cluster and multiplet analysis, spin system searches, resonance assignments, automated calculation of volumes in multidimensional spectra, calculation of distances with different approaches, including the full relaxation matrix approach, Bayesian analysis of peak features, correlation of molecular structures with NMR data, comparison of spectra via spectral algebra and pattern match techniques, automated sequential assignments on the basis of triple resonance spectra, and automatic strip calculation. In contrast to most other programs, many tasks are performed automatically.  相似文献   
28.
The lactose-specific phosphocarrier protein enzyme III of the bacterial phosphoenol-pyruvate-dependent phosphotransferase system of Staphylococcus aureus was modified by site-specific mutagenesis on the corresponding lacF gene in order to replace the histidine residues 78 and 82 of the amino acid sequence with a serine residue. Wild-type and both mutant genes were overexpressed in Escherichia coli and the gene products were purified to homogeneity. The conformation of wild-type and mutant proteins were monitored by 1H-NMR spectroscopy. In vitro phosphorylation studies on mutant lactose-specific enzyme III, as well as evidence from NMR spectroscopy, lead to the conclusion that His78 is the active-site for phosphorylation of lactose-specific enzyme III by phospho-HPr (histidine-containing protein). The role of His82 probably is the enhancement of velocity and efficiency of the phosphotransfer from lactose-specific enzyme III to lactose-specific enzyme II. This result refutes the conclusion of former work based on data by protelytic cleavage and sequencing of the 32P-labeled peptide of lactose-specific enzyme III that His82 is the active-site for phosphorylation.  相似文献   
29.
The termination of export processes from the nucleus to the cytoplasm in higher eukaryotes is mediated by binding of the small GTPase Ran as part of the export complexes to the Ran-binding domains (RanBD) of Ran-binding protein 2 (RanBP2) of the nuclear pore complex. So far, the structures of the first RanBD of RanBP2 and of RanBP1 in complexes with Ran have been known from X-ray crystallographic studies. Here we report the NMR solution structure of the uncomplexed second RanBD of RanBP2. The structure shows a pleckstrin homology (PH) fold featuring two almost orthogonal beta-sheets consisting of three and four strands and an alpha-helix sitting on top. This is in contrast to the RanBD in the crystal structure complexes in which one beta-strand is missing. That is probably due to the binding of the C-terminal alpha-helix of Ran to the RanBD in these complexes. To analyze the interaction between RanBD2 and the C terminus of Ran, NMR-titration studies with peptides comprising the six or 28 C-terminal residues of Ran were performed. While the six-residue peptide alone does not bind to RanBD2 in a specific manner, the 28-residue peptide, including the entire C-terminal helix of Ran, binds to RanBD2 in a manner analogous to the crystal structures. By solving the solution structure of the 28mer peptide alone, we confirmed that it adopts a stable alpha-helical structure like in native Ran and therefore serves as a valid model of the Ran C terminus. These results support current models that assume recognition of the transport complexes by the RanBDs through the Ran C terminus that is exposed in these complexes.  相似文献   
30.
A problem often encountered in multidimensional NMR-spectroscopy is that an existing chemical shift list of a protein has to be used to assign an experimental spectrum but does not fit sufficiently well for a safe assignment. A similar problem occurs when temperature or pressure series of n-dimensional spectra are to be evaluated automatically. We have developed two different algorithms, AUREMOL-SHIFTOPT1 and AUREMOL-SHIFTOPT2 that fulfill this task. In the present contribution their performance is analyzed employing a set of simulated and experimental two-dimensional and three-dimensional spectra obtained from three different proteins. A new z-score based on atom and amino acid specific chemical shift distributions is introduced to weight the chemical shift contributions in different dimensions properly.  相似文献   
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