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181.
Shovonlal Roy Sabyasachi Bhattacharya Partha Das Joydev Chattopadhyay 《Journal of biological physics》2007,33(1):1-17
We explore the mutual dependencies and interactions among different groups of species of the plankton population, based on
an analysis of the long-term field observations carried out by our group in the North–West coast of the Bay of Bengal. The
plankton community is structured into three groups of species, namely, non-toxic phytoplankton (NTP), toxic phytoplankton
(TPP) and zooplankton. To find the pair-wise dependencies among the three groups of plankton, Pearson and partial correlation
coefficients are calculated. To explore the simultaneous interaction among all the three groups, a time series analysis is
performed. Following an Expectation Maximization (E-M) algorithm, those data points which are missing due to irregularities
in sampling are estimated, and with the completed data set a Vector Auto-Regressive (VAR) model is analyzed. The overall analysis
demonstrates that toxin-producing phytoplankton play two distinct roles: the inhibition on consumption of toxic substances
reduces the abundance of zooplankton, and the toxic materials released by TPP significantly compensate for the competitive
disadvantages among phytoplankton species. Our study suggests that the presence of TPP might be a possible cause for the generation
of a complex interaction among the large number of phytoplankton and zooplankton species that might be responsible for the
prolonged coexistence of the plankton species in a fluctuating biomass. 相似文献
182.
Mareuil F Sizun C Perez J Schoenauer M Lallemand JY Bontems F 《European biophysics journal : EBJ》2007,37(1):95-104
Most proteins comprise several domains and/or participate in functional complexes. Owing to ongoing structural genomic projects,
it is likely that it will soon be possible to predict, with reasonable accuracy, the conserved regions of most structural
domains. Under these circumstances, it will be important to have methods, based on simple-to-acquire experimental data, that
allow to build and refine structures of multi-domain proteins or of protein complexes from homology models of the individual
domains/proteins. It has been recently shown that small angle X-ray scattering (SAXS) and NMR residual dipolar coupling (RDC)
data can be combined to determine the architecture of such objects when the X-ray structures of the domains are known and
can be considered as rigid objects. We developed a simple genetic algorithm to achieve the same goal, but by using homology
models of the domains considered as deformable objects. We applied it to two model systems, an S1KH bi-domain of the NusA
protein and the γS-crystallin protein. Despite its simplicity our algorithm is able to generate good solutions when driven
by SAXS and RDC data. 相似文献
183.
We develop an efficient stochastic simulation algorithm for analyzing actin filament growth and decay in the presence of various actin-binding proteins. The evolution of nucleotide profiles of filaments can be tracked and the resulting feedback to actin-binding proteins is incorporated. The computational efficiency of the new method enables us to focus on experimentally realistic problems, and as one example we use it to analyze the experimental data of Helfer et al. [(2006). Mammalian twinfilin sequesters ADP-G-actin and caps filament barbed ends: implications in motility. EMBO J. 25, 1184-1195] on the capping and G-actin sequestering activity of twinfilin. We show that the binding specificity of twinfilin for ADP-G-actin is crucial for the observed biphasic evolution of the filament length distribution in the presence of twinfilin, and we demonstrate that twinfilin can be an essential part of the molecular machinery for regulating filament lengths after a short burst of polymerization. Significantly, our simulations indicate that the pyrenyl-actin fluorescence experiments would fail to report the emergence of large filaments under certain experimental conditions. 相似文献
184.
The use of multiple hypothesis testing procedures has been receiving a lot of attention recently by statisticians in DNA microarray analysis. The traditional FWER controlling procedures are not very useful in this situation since the experiments are exploratory by nature and researchers are more interested in controlling the rate of false positives rather than controlling the probability of making a single erroneous decision. This has led to increased use of FDR (False Discovery Rate) controlling procedures. Genovese and Wasserman proposed a single-step FDR procedure that is an asymptotic approximation to the original Benjamini and Hochberg stepwise procedure. In this paper, we modify the Genovese-Wasserman procedure to force the FDR control closer to the level alpha in the independence setting. Assuming that the data comes from a mixture of two normals, we also propose to make this procedure adaptive by first estimating the parameters using the EM algorithm and then using these estimated parameters into the above modification of the Genovese-Wasserman procedure. We compare this procedure with the original Benjamini-Hochberg and the SAM thresholding procedures. The FDR control and other properties of this adaptive procedure are verified numerically. 相似文献
185.
从植物资源、化合物骨架结构、波谱特征及生物活性等方面,综述了国内外报导的38个喹诺酸类型三萜化合物。 相似文献
186.
187.
Gueguim-Kana EB Oloke JK Lateef A Zebaze-Kana MG 《Journal of industrial microbiology & biotechnology》2007,34(7):491-496
The acidification behavior of Lactobacillus bulgaricus and Streptococcus thermophilus for yoghurt production was investigated along temperature profiles within the optimal window of 38–44 °C. For the optimal
acidification temperature profile search, an optimization engine module built on a modular artificial neural network (ANN)
and genetic algorithm (GA) was used. Fourteen batches of yoghurt fermentations were evaluated using different temperature
profiles in order to train and validate the ANN sub-module. The ANN captured the nonlinear relationship between temperature
profiles and acidification patterns on training data after 150 epochs. This served as an evaluation function for the GA. The
acidification slope of the temperature profile was the performance index. The GA sub-module iteratively evolved better temperature
profiles across generations using GA operations. The stopping criterion was met after 11 generations. The optimal profile
showed an acidification slope of 0.06117 compared to an initial value of 0.0127 and at a set point sequence of 43, 38, 44,
43, and 39 °C. Laboratory evaluation of three replicates of the GA suggested optimum profile of 43, 38, 44, 43, and 39 °C
gave an average slope of 0.04132. The optimization engine used (to be published elsewhere) could effectively search for optimal
profiles of different physico-chemical parameters of fermentation processes. 相似文献
188.
It has been proposed that proteins fold by a process called "Zipping and Assembly" (Z&A). Zipping refers to the growth of local substructures within the chain, and assembly refers to the coming together of already-formed pieces. Our interest here is in whether Z&A is a general method that can fold most of sequence space, to global minima, efficiently. Using the HP model, we can address this question by enumerating full conformation and sequence spaces. We find that Z&A reaches the global energy minimum native states, even though it searches only a very small fraction of conformational space, for most sequences in the full sequence space. We find that Z&A, a mechanism-based search, is more efficient in our tests than the replica exchange search method. Folding efficiency is increased for chains having: (a) small loop-closure steps, consistent with observations by Plaxco et al. 1998;277;985-994 that folding rates correlate with contact order, (b) neither too few nor too many nucleation sites per chain, and (c) assembly steps that do not occur too early in the folding process. We find that the efficiency increases with chain length, although our range of chain lengths is limited. We believe these insights may be useful for developing faster protein conformational search algorithms. 相似文献
189.
Bublil EM Freund NT Mayrose I Penn O Roitburd-Berman A Rubinstein ND Pupko T Gershoni JM 《Proteins》2007,68(1):294-304
Mapping the epitope of an antibody is of great interest, since it contributes much to our understanding of the mechanisms of molecular recognition and provides the basis for rational vaccine design. Here we present Mapitope, a computer algorithm for epitope mapping. The algorithm input is a set of affinity isolated peptides obtained by screening phage display peptide-libraries with the antibody of interest. The output is usually 1-3 epitope candidates on the surface of the atomic structure of the antigen. We have systematically tested the performance of Mapitope by assessing the effect of the algorithm parameters on the final prediction. Thus, we have examined the effect of the statistical threshold (ST) parameter, relating to the frequency distribution and enrichment of amino acid pairs from the isolated peptides and the D (distance) and E (exposure) parameters which relate to the physical parameters of the antigen. Two model systems were analyzed in which the antibody of interest had previously been co-crystallized with the antigen and thus the epitope is a given. The Mapitope algorithm successfully predicted the epitopes in both models. Accordingly, we formulated a stepwise paradigm for the prediction of discontinuous conformational epitopes using peptides obtained from screening phage display libraries. We applied this paradigm to successfully predict the epitope of the Trastuzumab antibody on the surface of the Her-2/neu receptor in a third model system. 相似文献
190.
Disulfide bonds play an important role in stabilizing protein structure and regulating protein function. Therefore, the ability to infer disulfide connectivity from protein sequences will be valuable in structural modeling and functional analysis. However, to predict disulfide connectivity directly from sequences presents a challenge to computational biologists due to the nonlocal nature of disulfide bonds, i.e., the close spatial proximity of the cysteine pair that forms the disulfide bond does not necessarily imply the short sequence separation of the cysteine residues. Recently, Chen and Hwang (Proteins 2005;61:507-512) treated this problem as a multiple class classification by defining each distinct disulfide pattern as a class. They used multiple support vector machines based on a variety of sequence features to predict the disulfide patterns. Their results compare favorably with those in the literature for a benchmark dataset sharing less than 30% sequence identity. However, since the number of disulfide patterns grows rapidly when the number of disulfide bonds increases, their method performs unsatisfactorily for the cases of large number of disulfide bonds. In this work, we propose a novel method to represent disulfide connectivity in terms of cysteine pairs, instead of disulfide patterns. Since the number of bonding states of the cysteine pairs is independent of that of disulfide bonds, the problem of class explosion is avoided. The bonding states of the cysteine pairs are predicted using the support vector machines together with the genetic algorithm optimization for feature selection. The complete disulfide patterns are then determined from the connectivity matrices that are constructed from the predicted bonding states of the cysteine pairs. Our approach outperforms the current approaches in the literature. 相似文献